JabRef References output

BibTeX-Key	Author / Editor / Organization	Title	Year	Journal / Proceedings / Book	BibTeX type	Keywords
Agr04	Agris, P.F.	Decoding the genome: a modified view [Abstract] [BibTeX] [URL] [PDF]	2004	Nucleic Acids Res. Vol. 32 (1) , pp. 223-38	article	genetic
Abstract: Transfer RNA's role in decoding the genome is critical to the accuracy and efficiency of protein synthesis. Though modified nucleosides were identified in RNA 50 years ago, only recently has their importance to tRNA's ability to decode cognate and wobble codons become apparent. RNA modifications are ubiquitous. To date, some 100 different posttranslational modifications have been identified. Modifications of tRNA are the most extensively investigated; however, many other RNAs have modified nucleosides. The modifications that occur at the first, or wobble position, of tRNA's anticodon and those 3'-adjacent to the anticodon are of particular interest. The tRNAs most affected by individual and combinations of modifications respond to codons in mixed codon boxes where distinction of the third codon base is important for discriminating between the correct cognate or wobble codons and the incorrect near-cognate codons (e.g. AAA/G for lysine versus AAU/C asparagine). In contrast, other modifications expand wobble codon recognition, such as U*U base pairing, for tRNAs that respond to multiple codons of a 4-fold degenerate codon box (e.g. GUU/A/C/G for valine). Whether restricting codon recognition, expanding wobble, enabling translocation, or maintaining the messenger RNA, reading frame modifications appear to reduce anticodon loop dynamics to that accepted by the ribosome. Therefore, we suggest that anticodon stem and loop domain nucleoside modifications allow a limited number of tRNAs to accurately and efficiently decode the 61 amino acid codons by selectively restricting some anticodon-codon interactions and expanding others.
BibTeX: @article{Agr04, author = {Agris, Paul F}, title = {Decoding the genome: a modified view}, journal = {Nucleic Acids Res.}, year = {2004}, volume = {32}, number = {1}, pages = {223--38}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=384350&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1093/nar/gkh185} }
AloWil05	Alonso, C.R. & Wilkins, A.S.	The molecular elements that underlie developmental evolution [BibTeX] [PDF]	2005	Nat. Rev. Genet. Vol. 6 (September) , pp. 709-715	article	embryology, developmental
BibTeX: @article{AloWil05, author = {Alonso, Claudio R and Wilkins, Adam S}, title = {The molecular elements that underlie developmental evolution}, journal = {Nat. Rev. Genet.}, year = {2005}, volume = {6}, number = {September}, pages = {709--715} }
AraLiHar09	Arai, J. a.; Li, S.; Hartley, D.M. & Feig, L. a.	Transgenerational rescue of a genetic defect in long-term potentiation and memory formation by juvenile enrichment [Abstract] [BibTeX] [URL] [PDF]	2009	J. Neurosci. Vol. 29 (5) , pp. 1496-502	article	neural
Abstract: The idea that qualities acquired from experience can be transmitted to future offspring has long been considered incompatible with current understanding of genetics. However, the recent documentation of non-Mendelian transgenerational inheritance makes such a "Lamarckian"-like phenomenon more plausible. Here, we demonstrate that exposure of 15-d-old mice to 2 weeks of an enriched environment (EE), that includes exposure to novel objects, elevated social interactions and voluntary exercise, enhances long-term potentiation (LTP) not only in these enriched mice but also in their future offspring through early adolescence, even if the offspring never experience EE. In both generations, LTP induction is augmented by a newly appearing cAMP/p38 MAP kinase-dependent signaling cascade. Strikingly, defective LTP and contextual fear conditioning memory normally associated with ras-grf knock-out mice are both masked in the offspring of enriched mutant parents. The transgenerational transmission of this effect occurs from the enriched mother to her offspring during embryogenesis. If a similar phenomenon occurs in humans, the effectiveness of one's memory during adolescence, particularly in those with defective cell signaling mechanisms that control memory, can be influenced by environmental stimulation experienced by one's mother during her youth.
BibTeX: @article{AraLiHar09, author = {Arai, Junko a and Li, Shaomin and Hartley, Dean M and Feig, Larry a}, title = {Transgenerational rescue of a genetic defect in long-term potentiation and memory formation by juvenile enrichment}, journal = {J. Neurosci.}, year = {2009}, volume = {29}, number = {5}, pages = {1496--502}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19193896}, doi = {http://dx.doi.org/10.1523/JNEUROSCI.5057-08.2009} }
AriHay06	Arias, A.M. & Hayward, P.	Filtering transcriptional noise during development: concepts and mechanisms [Abstract] [BibTeX] [URL] [PDF]	2006	Nat. Rev. Genet. Vol. 7 (1) , pp. 34-44	article	embryology, developmental
Abstract: The assignation of cell fates during eukaryotic development relies on the coordinated and stable expression of cohorts of genes within cell populations. The precise and reproducible nature of this process is remarkable given that, at the single-cell level, the transcription of individual genes is associated with noise - random molecular fluctuations that create variability in the levels of gene expression within a cell population. Here we consider the implications of transcriptional noise for development and suggest the existence of molecular devices that are dedicated to filtering noise. On the basis of existing evidence, we propose that one such mechanism might depend on the Wnt signalling pathway.
BibTeX: @article{AriHay06, author = {Arias, Alfonso Martinez and Hayward, Penelope}, title = {Filtering transcriptional noise during development: concepts and mechanisms}, journal = {Nat. Rev. Genet.}, year = {2006}, volume = {7}, number = {1}, pages = {34--44}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16369570}, doi = {http://dx.doi.org/10.1038/nrg1750} }
BKreHar08	Bártová, E.; Krejc, J.; Harnicarová, A.; Galiová, G. & Kozubek, S.	Histone modifications and nuclear architecture: a review [Abstract] [BibTeX] [URL] [PDF]	2008	J. Histochem. Cytochem. Vol. 56 (8) , pp. 711-21	article	histone
Abstract: Epigenetic modifications, such as acetylation, phosphorylation, methylation, ubiquitination, and ADP ribosylation, of the highly conserved core histones, H2A, H2B, H3, and H4, influence the genetic potential of DNA. The enormous regulatory potential of histone modification is illustrated in the vast array of epigenetic markers found throughout the genome. More than the other types of histone modification, acetylation and methylation of specific lysine residues on N-terminal histone tails are fundamental for the formation of chromatin domains, such as euchromatin, and facultative and constitutive heterochromatin. In addition, the modification of histones can cause a region of chromatin to undergo nuclear compartmentalization and, as such, specific epigenetic markers are non-randomly distributed within interphase nuclei. In this review, we summarize the principles behind epigenetic compartmentalization and the functional consequences of chromatin arrangement within interphase nuclei.
BibTeX: @article{BKreHar08, author = {Bártová, Eva and Krejc, Jana and Harnicarová, Andrea and Galiová, Gabriela and Kozubek, Stanislav}, title = {Histone modifications and nuclear architecture: a review}, journal = {J. Histochem. Cytochem.}, year = {2008}, volume = {56}, number = {8}, pages = {711--21}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2443610&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1369/jhc.2008.951251} }
BabHayWra07	Babbitt, C.C.; Haygood, R. & Wray, G.	When two is better than one [Abstract] [BibTeX] [URL] [PDF]	2007	Cell Vol. 131 (2) , pp. 225-7	article	embryology, developmental
Abstract: Gene duplication and divergence has long been considered an important route to adaptation and phenotypic evolution. Reporting in Nature, Hittinger and Carroll (2007) provide the first clear example of adaptations in both regulatory regions and protein-coding regions after gene duplication. This combination of evolutionary changes appears to have resolved an adaptive conflict, leading to increased organismal fitness.
BibTeX: @article{BabHayWra07, author = {Babbitt, Courtney C and Haygood, Ralph and Wray, Gregory}, title = {When two is better than one}, journal = {Cell}, year = {2007}, volume = {131}, number = {2}, pages = {225--7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17956721}, doi = {http://dx.doi.org/10.1016/j.cell.2007.10.001} }
BadMitBea06	Badano, J.L.; Mitsuma, N.; Beales, P.L. & Katsanis, N.	The ciliopathies: an emerging class of human genetic disorders [Abstract] [BibTeX] [URL] [PDF]	2006	Annu. Rev. Genomics Hum. Genet. Vol. 7 , pp. 125-48	article	genetic
Abstract: Cilia and flagella are ancient, evolutionarily conserved organelles that project from cell surfaces to perform diverse biological roles, including whole-cell locomotion; movement of fluid; chemo-, mechano-, and photosensation; and sexual reproduction. Consistent with their stringent evolutionary conservation, defects in cilia are associated with a range of human diseases, such as primary ciliary dyskinesia, hydrocephalus, polycystic liver and kidney disease, and some forms of retinal degeneration. Recent evidence indicates that ciliary defects can lead to a broader set of developmental and adult phenotypes, with mutations in ciliary proteins now associated with nephronophthisis, Bardet-Biedl syndrome, Alstrom syndrome, and Meckel-Gruber syndrome. The molecular data linking seemingly unrelated clinical entities are beginning to highlight a common theme, where defects in ciliary structure and function can lead to a predictable phenotypic pattern that has potentially predictive and therapeutic value.
BibTeX: @article{BadMitBea06, author = {Badano, Jose L and Mitsuma, Norimasa and Beales, Phil L and Katsanis, Nicholas}, title = {The ciliopathies: an emerging class of human genetic disorders}, journal = {Annu. Rev. Genomics Hum. Genet.}, year = {2006}, volume = {7}, pages = {125--48}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16722803}, doi = {http://dx.doi.org/10.1146/annurev.genom.7.080505.115610} }
BakAllWan08	Baker, L. a.; Allis, C.D. & Wang, G.G.	PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks [Abstract] [BibTeX] [URL] [PDF]	2008	Mutat. Res. Vol. 647 (1-2) , pp. 3-12	article	histone
Abstract: Histone covalent modifications regulate many, if not all, DNA-templated processes, including gene expression and DNA damage response. The biological consequences of histone modifications are mediated partially by evolutionarily conserved "reader/effector" modules that bind to histone marks in a modification- and context-specific fashion and subsequently enact chromatin changes or recruit other proteins to do so. Recently, the Plant Homeodomain (PHD) finger has emerged as a class of specialized "reader" modules that, in some instances, recognize the methylation status of histone lysine residues, such as histone H3 lysine 4 (H3K4). While mutations in catalytic enzymes that mediate the addition or removal of histone modifications (i.e., "writers" and "erasers") are already known to be involved in various human diseases, mutations in the modification-specific "reader" proteins are only beginning to be recognized as contributing to human diseases. For instance, point mutations, deletions or chromosomal translocations that target PHD fingers encoded by many genes (such as recombination activating gene 2 (RAG2), Inhibitor of Growth (ING), nuclear receptor-binding SET domain-containing 1 (NSD1) and Alpha Thalassaemia and Mental Retardation Syndrome, X-linked (ATRX)) have been associated with a wide range of human pathologies including immunological disorders, cancers, and neurological diseases. In this review, we will discuss the structural features of PHD fingers as well as the diseases for which direct mutation or dysregulation of the PHD finger has been reported. We propose that misinterpretation of the epigenetic marks may serve as a general mechanism for human diseases of this category. Determining the regulatory roles of histone covalent modifications in the context of human disease will allow for a more thorough understanding of normal and pathological development, and may provide innovative therapeutic strategies wherein "chromatin readers" stand as potential drug targets.
BibTeX: @article{BakAllWan08, author = {Baker, Lindsey a and Allis, C David and Wang, Gang G}, title = {PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks}, journal = {Mutat. Res.}, year = {2008}, volume = {647}, number = {1-2}, pages = {3--12}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2656448&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1016/j.mrfmmm.2008.07.004} }
BakGra05	Baker, S.P. & Grant, P. a.	The proteasome: not just degrading anymore [Abstract] [BibTeX] [URL] [PDF]	2005	Cell Vol. 123 (3) , pp. 361-3	article	epigenetic
Abstract: The proteasome is a large multiprotein complex that has a critical role in the degradation of ubiquitylated proteins. A fascinating paper in this issue of Cell (Lee et al., 2005) now reveals that the proteasome recruits the SAGA histone acetyltransferase complex to a target promoter during gene activation. This finding adds to the growing body of evidence indicating that the proteasome has nonproteolytic functions.
BibTeX: @article{BakGra05, author = {Baker, Stephen P and Grant, Patrick a}, title = {The proteasome: not just degrading anymore}, journal = {Cell}, year = {2005}, volume = {123}, number = {3}, pages = {361--3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16269325}, doi = {http://dx.doi.org/10.1016/j.cell.2005.10.013} }
BarCalGao10	Barash, Y.; Calarco, J. a.; Gao, W.; Pan, Q.; Wang, X.; Shai, O.; Blencowe, B.J. & Frey, B.J.	Deciphering the splicing code [Abstract] [BibTeX] [URL] [PDF]	2010	Nature Vol. 465 (7294) , pp. 53-9	article	splicing
Abstract: Alternative splicing has a crucial role in the generation of biological complexity, and its misregulation is often involved in human disease. Here we describe the assembly of a 'splicing code', which uses combinations of hundreds of RNA features to predict tissue-dependent changes in alternative splicing for thousands of exons. The code determines new classes of splicing patterns, identifies distinct regulatory programs in different tissues, and identifies mutation-verified regulatory sequences. Widespread regulatory strategies are revealed, including the use of unexpectedly large combinations of features, the establishment of low exon inclusion levels that are overcome by features in specific tissues, the appearance of features deeper into introns than previously appreciated, and the modulation of splice variant levels by transcript structure characteristics. The code detected a class of exons whose inclusion silences expression in adult tissues by activating nonsense-mediated messenger RNA decay, but whose exclusion promotes expression during embryogenesis. The code facilitates the discovery and detailed characterization of regulated alternative splicing events on a genome-wide scale.
BibTeX: @article{BarCalGao10, author = {Barash, Yoseph and Calarco, John a and Gao, Weijun and Pan, Qun and Wang, Xinchen and Shai, Ofer and Blencowe, Benjamin J and Frey, Brendan J}, title = {Deciphering the splicing code}, journal = {Nature}, publisher = {Nature Publishing Group}, year = {2010}, volume = {465}, number = {7294}, pages = {53--9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20445623}, doi = {http://dx.doi.org/10.1038/nature09000} }
Bar11	Barbieri, M.	Origin and evolution of the brain [BibTeX] [PDF]	2011	Biosemiotics Vol. 4 (3) , pp. 369-399	article	developmental, neural, brain
BibTeX: @article{Bar11, author = {Barbieri, M.}, title = {Origin and evolution of the brain}, journal = {Biosemiotics}, publisher = {Springer}, year = {2011}, volume = {4}, number = {3}, pages = {369--399} }
Bar08	Barbieri, M.	Biosemiotics: a new understanding of life [BibTeX] [PDF]	2008	Naturwissenschaften Vol. 95 (7) , pp. 577-599	article	biosemiotics
BibTeX: @article{Bar08, author = {Barbieri, M.}, title = {Biosemiotics: a new understanding of life}, journal = {Naturwissenschaften}, publisher = {Springer}, year = {2008}, volume = {95}, number = {7}, pages = {577--599} }
BenHajMoo08	Bender, A.; Hajieva, P. & Moosmann, B.	Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria [Abstract] [BibTeX] [URL] [PDF]	2008	Proc. Natl. Acad. Sci. U.S.A. Vol. 105 (43) , pp. 16496-501	article	genetic
Abstract: Humans and most other animals use 2 different genetic codes to translate their hereditary information: the standard code for nuclear-encoded proteins and a modern variant of this code in mitochondria. Despite the pivotal role of the genetic code for cell biology, the functional significance of the deviant mitochondrial code has remained enigmatic since its first description in 1979. Here, we show that profound and functionally beneficial alterations on the encoded protein level were causative for the AUA codon reassignment from isoleucine to methionine observed in most mitochondrial lineages. We demonstrate that this codon reassignment leads to a massive accumulation of the easily oxidized amino acid methionine in the highly oxidative inner mitochondrial membrane. This apparently paradoxical outcome can yet be smoothly settled if the antioxidant surface chemistry of methionine is taken into account, and we present direct experimental evidence that intramembrane accumulation of methionine exhibits antioxidant and cytoprotective properties in living cells. Our results unveil that methionine is an evolutionarily selected antioxidant building block of respiratory chain complexes. Collective protein alterations can thus constitute the selective advantage behind codon reassignments, which authenticates the "ambiguous decoding" hypothesis of genetic code evolution. Oxidative stress has shaped the mitochondrial genetic code.
BibTeX: @article{BenHajMoo08, author = {Bender, Aline and Hajieva, Parvana and Moosmann, Bernd}, title = {Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2008}, volume = {105}, number = {43}, pages = {16496--501}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2575448&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1073/pnas.0802779105} }
Ber07	Berger, S.L.	The complex language of chromatin regulation during transcription [Abstract] [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 407-12	article	epigenetic
Abstract: An important development in understanding the influence of chromatin on gene regulation has been the finding that DNA methylation and histone post-translational modifications lead to the recruitment of protein complexes that regulate transcription. Early interpretations of this phenomenon involved gene regulation reflecting predictive activating or repressing types of modification. However, further exploration reveals that transcription occurs against a backdrop of mixtures of complex modifications, which probably have several roles. Although such modifications were initially thought to be a simple code, a more likely model is of a sophisticated, nuanced chromatin 'language' in which different combinations of basic building blocks yield dynamic functional outcomes.
BibTeX: @article{Ber07, author = {Berger, Shelley L}, title = {The complex language of chromatin regulation during transcription}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {407--12}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17522673}, doi = {http://dx.doi.org/10.1038/nature05915} }
BerMeiLan07	Bernstein, B.E.; Meissner, A. & Lander, E.S.	The mammalian epigenome [Abstract] [BibTeX] [URL] [PDF]	2007	Cell Vol. 128 (4) , pp. 669-81	article	epigenetic
Abstract: Chemical modifications to DNA and histone proteins form a complex regulatory network that modulates chromatin structure and genome function. The epigenome refers to the complete description of these potentially heritable changes across the genome. The composition of the epigenome within a given cell is a function of genetic determinants, lineage, and environment. With the sequencing of the human genome completed, investigators now seek a comprehensive view of the epigenetic changes that determine how genetic information is made manifest across an incredibly varied background of developmental stages, tissue types, and disease states. Here we review current research efforts, with an emphasis on large-scale studies, emerging technologies, and challenges ahead.
BibTeX: @article{BerMeiLan07, author = {Bernstein, Bradley E and Meissner, Alexander and Lander, Eric S}, title = {The mammalian epigenome}, journal = {Cell}, year = {2007}, volume = {128}, number = {4}, pages = {669--81}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17320505}, doi = {http://dx.doi.org/10.1016/j.cell.2007.01.033} }
BiaKerYan04	Bialek, P.; Kern, B.; Yang, X.; Schrock, M.; Sosic, D.; Hong, N.; Wu, H.; Yu, K.; Ornitz, D.M.; Olson, E.N.; Justice, M.J. & Karsenty, G.	A twist code determines the onset of osteoblast differentiation bone [BibTeX] [PDF]	2004	Dev. Cell Vol. 6 , pp. 423-435	article	embryology, developmental
BibTeX: @article{BiaKerYan04, author = {Bialek, Peter and Kern, Britt and Yang, Xiangli and Schrock, Marijke and Sosic, Drazen and Hong, Nancy and Wu, Hua and Yu, Kai and Ornitz, David M and Olson, Eric N and Justice, Monica J and Karsenty, Gerard}, title = {A twist code determines the onset of osteoblast differentiation bone}, journal = {Dev. Cell}, year = {2004}, volume = {6}, pages = {423--435} }
Bir07	Bird, A.	Perceptions of epigenetics [Abstract] [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 396-8	article	epigenetic
Abstract: Geneticists study the gene; however, for epigeneticists, there is no obvious 'epigene'. Nevertheless, during the past year, more than 2,500 articles, numerous scientific meetings and a new journal were devoted to the subject of epigenetics. It encompasses some of the most exciting contemporary biology and is portrayed by the popular press as a revolutionary new science--an antidote to the idea that we are hard-wired by our genes. So what is epigenetics?
BibTeX: @article{Bir07, author = {Bird, Adrian}, title = {Perceptions of epigenetics}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {396--8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17522671}, doi = {http://dx.doi.org/10.1038/nature05913} }
BleKha07	Blencowe, B.J. & Khanna, M.	Molecular biology: RNA in control [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 391-3	article	rna
BibTeX: @article{BleKha07, author = {Blencowe, Benjamin J and Khanna, May}, title = {Molecular biology: RNA in control}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {391--3}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17522667}, doi = {http://dx.doi.org/10.1038/447391a} }
BolVetKis07	Bollenbach, T.; Vetsigian, K. & Kishony, R.	Evolution and multilevel optimization of the genetic code [Abstract] [BibTeX] [URL] [PDF]	2007	Genome Res. Vol. 17 (4) , pp. 401-4	article	genetic
Abstract: The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors.
BibTeX: @article{BolVetKis07, author = {Bollenbach, Tobias and Vetsigian, Kalin and Kishony, Roy}, title = {Evolution and multilevel optimization of the genetic code}, journal = {Genome Res.}, year = {2007}, volume = {17}, number = {4}, pages = {401--4}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17351130}, doi = {http://dx.doi.org/10.1101/gr.6144007} }
BorNesAll08	Borrelli, E.; Nestler, E.J.; Allis, C.D. & Sassone-Corsi, P.	Decoding the epigenetic language of neuronal plasticity [Abstract] [BibTeX] [URL] [PDF]	2008	Neuron Vol. 60 (6) , pp. 961-74	article	histone
Abstract: Neurons are submitted to an exceptional variety of stimuli and are able to convert these into high-order functions, such as storing memories, controlling behavior, and governing consciousness. These unique properties are based on the highly flexible nature of neurons, a characteristic that can be regulated by the complex molecular machinery that controls gene expression. Epigenetic control, which largely involves events of chromatin remodeling, appears to be one way in which transcriptional regulation of gene expression can be modified in neurons. This review will focus on how epigenetic control in the mature nervous system may guide dynamic plasticity processes and long-lasting cellular neuronal responses. We outline the molecular pathways underlying chromatin transitions, propose the presence of an "epigenetic indexing code," and discuss how central findings accumulating at an exponential pace in the field of epigenetics are conceptually changing our perspective of adult brain function.
BibTeX: @article{BorNesAll08, author = {Borrelli, Emiliana and Nestler, Eric J and Allis, C David and Sassone-Corsi, Paolo}, title = {Decoding the epigenetic language of neuronal plasticity}, journal = {Neuron}, publisher = {Elsevier Inc.}, year = {2008}, volume = {60}, number = {6}, pages = {961--74}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2737473&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1016/j.neuron.2008.10.012} }
BouMikNur05	Boutanaev, A.M.; Mikhaylova, L.M. & Nurminsky, D.I.	The pattern of chromosome folding in interphase is outlined by the linear gene density profile [BibTeX] [PDF]	2005	Mol. Cell. Biol. Vol. 25 (18) , pp. 8379-8386	article	folding
BibTeX: @article{BouMikNur05, author = {Boutanaev, Alexander M and Mikhaylova, Lyudmila M and Nurminsky, Dmitry I}, title = {The pattern of chromosome folding in interphase is outlined by the linear gene density profile}, journal = {Mol. Cell. Biol.}, year = {2005}, volume = {25}, number = {18}, pages = {8379--8386}, doi = {http://dx.doi.org/10.1128/MCB.25.18.8379} }
BraHas09	Brandon, M.P. & Hasselmo, M.E.	Sources of the spatial code within the hippocampus [Abstract] [BibTeX] [URL] [PDF]	2009	F1000 Biol. Rep. Vol. 1 (January) , pp. 3	article	neural
Abstract: Neurons in the hippocampus are thought to provide information on an animal's location within its environment. Input to the hippocampus comes via afferents from the entorhinal cortex, which are separated into several major pathways serving different hippocampal regions. Recent studies show the significance of individual afferent pathways in location perception, enhancing our understanding of hippocampal function.
BibTeX: @article{BraHas09, author = {Brandon, Mark P and Hasselmo, Michael E}, title = {Sources of the spatial code within the hippocampus}, journal = {F1000 Biol. Rep.}, year = {2009}, volume = {1}, number = {January}, pages = {3}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2920688&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.3410/B1-3} }
BriPieJes00	Briscoe, J.; Pierani, a.; Jessell, T.M. & Ericson, J.	A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube [Abstract] [BibTeX] [URL] [PDF]	2000	Cell Vol. 101 (4) , pp. 435-45	article	neural
Abstract: Distinct classes of neurons are generated at defined positions in the ventral neural tube in response to a gradient of Sonic Hedgehog (Shh) activity. A set of homeodomain transcription factors expressed by neural progenitors act as intermediaries in Shh-dependent neural patterning. These homeodomain factors fall into two classes: class I proteins are repressed by Shh and class II proteins require Shh signaling for their expression. The profile of class I and class II protein expression defines five progenitor domains, each of which generates a distinct class of postmitotic neurons. Cross-repressive interactions between class I and class II proteins appear to refine and maintain these progenitor domains. The combinatorial expression of three of these proteins--Nkx6.1, Nkx2.2, and Irx3--specifies the identity of three classes of neurons generated in the ventral third of the neural tube.
BibTeX: @article{BriPieJes00, author = {Briscoe, J and Pierani, a and Jessell, T M and Ericson, J}, title = {A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube}, journal = {Cell}, year = {2000}, volume = {101}, number = {4}, pages = {435--45}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10830170} }
ByrMorHum10	Byron, A.; Morgan, M.R. & Humphries, M.J.	Adhesion signalling complexes [Abstract] [BibTeX] [URL] [PDF]	2010	Curr. Biol. Vol. 20 (24) , pp. R1063-7	article	adhesion
Abstract: Intercellular communication in metazoa not only requires autocrine, paracrine and exocrine signalling systems, but it also relies on the structural and positional information encoded in extracellular matrices (ECMs). Most cells in tissues are structurally and functionally integrated with their surrounding ECM in a highly organised manner involving thousands of dynamic connections. On the intracellular face of these linkages, adhesion receptors - principally integrins and syndecans - link the cytoskeleton to the plasma membrane and compartmentalise cytoplasmic signalling events, whereas at the extracellular face the same receptors direct and organise the deposition of the ECM itself. Adhesion receptors transduce mechanical force bidirectionally across the plasma membrane by tethering variably deformable ECMs to the contractile cytoskeleton (Figure 1), and they translate the topography and composition of the ECM into chemical signals that determine behaviour. The membrane-proximal functions of adhesion receptors in turn trigger distal processes within cells, such as alterations in the direction of cell movement and the regulation of gene transcription, and long-range effects outside cells, such as the construction of ECM networks and consequent shaping of higher-order tissue structure. Given the diverse and fundamental roles attributed to adhesion, it is understandable that adhesion receptor engagement has been reported to alter the flux through virtually all major signalling pathways.
BibTeX: @article{ByrMorHum10, author = {Byron, Adam and Morgan, Mark R and Humphries, Martin J}, title = {Adhesion signalling complexes}, journal = {Curr. Biol.}, publisher = {Elsevier}, year = {2010}, volume = {20}, number = {24}, pages = {R1063--7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21172621}, doi = {http://dx.doi.org/10.1016/j.cub.2010.10.059} }
CanCanSch10	Cannarozzi, G.; Cannarrozzi, G.; Schraudolph, N.N.; Faty, M.; von Rohr, P.; Friberg, M.T.; Roth, A.C.; Gonnet, P.; Gonnet, G. & Barral, Y.	A role for codon order in translation dynamics [Abstract] [BibTeX] [URL] [PDF]	2010	Cell Vol. 141 (2) , pp. 355-67	article	genetic
Abstract: The genetic code is degenerate. Each amino acid is encoded by up to six synonymous codons; the choice between these codons influences gene expression. Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use the same tRNA. The effect is pronounced in rapidly induced genes, involves both frequent and rare codons and diminishes only slowly as a function of the distance between subsequent synonymous codons. Furthermore, we found that in S. cerevisiae codon correlation accelerates translation relative to the translation of synonymous yet anticorrelated sequences. The data suggest that tRNA diffusion away from the ribosome is slower than translation, and that some tRNA channeling takes place at the ribosome. They also establish that the dynamics of translation leave a significant signature at the level of the genome.
BibTeX: @article{CanCanSch10, author = {Cannarozzi, Gina and Cannarrozzi, Gina and Schraudolph, Nicol N and Faty, Mahamadou and von Rohr, Peter and Friberg, Markus T and Roth, Alexander C and Gonnet, Pedro and Gonnet, Gaston and Barral, Yves}, title = {A role for codon order in translation dynamics}, journal = {Cell}, publisher = {Elsevier Ltd}, year = {2010}, volume = {141}, number = {2}, pages = {355--67}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20403329}, doi = {http://dx.doi.org/10.1016/j.cell.2010.02.036} }
CasLarAnd07	Caspary, T.; Larkins, C.E. & Anderson, K.V.	The graded response to Sonic Hedgehog depends on cilia architecture [Abstract] [BibTeX] [URL] [PDF]	2007	Dev. Cell Vol. 12 (5) , pp. 767-78	article	embryology, developmental
Abstract: Several studies have linked cilia and Hedgehog signaling, but the precise roles of ciliary proteins in signal transduction remain enigmatic. Here we describe a mouse mutation, hennin (hnn), that causes coupled defects in cilia structure and Sonic hedgehog (Shh) signaling. The hnn mutant cilia are short with a specific defect in the structure of the ciliary axoneme, and the hnn neural tube shows a Shh-independent expansion of the domain of motor neuron progenitors. The hnn mutation is a null allele of Arl13b, a small GTPase of the Arf/Arl family, and the Arl13b protein is localized to cilia. Double mutant analysis indicates that Gli3 repressor activity is normal in hnn embryos, but Gli activators are constitutively active at low levels. Thus, normal structure of the ciliary axoneme is required for the cell to translate different levels of Shh ligand into differential regulation of the Gli transcription factors that implement Hedgehog signals.
BibTeX: @article{CasLarAnd07, author = {Caspary, Tamara and Larkins, Christine E and Anderson, Kathryn V}, title = {The graded response to Sonic Hedgehog depends on cilia architecture}, journal = {Dev. Cell}, year = {2007}, volume = {12}, number = {5}, pages = {767--78}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17488627}, doi = {http://dx.doi.org/10.1016/j.devcel.2007.03.004} }
ChaHemBar08	Chang, H.H.; Hemberg, M.; Barahona, M.; Ingber, D.E. & Huang, S.	Transcriptome-wide noise controls lineage choice in mammalian progenitor cells [Abstract] [BibTeX] [URL] [PDF]	2008	Nature Vol. 453 (7194) , pp. 544-7	article	embryology, developmental
Abstract: Phenotypic cell-to-cell variability within clonal populations may be a manifestation of 'gene expression noise', or it may reflect stable phenotypic variants. Such 'non-genetic cell individuality' can arise from the slow fluctuations of protein levels in mammalian cells. These fluctuations produce persistent cell individuality, thereby rendering a clonal population heterogeneous. However, it remains unknown whether this heterogeneity may account for the stochasticity of cell fate decisions in stem cells. Here we show that in clonal populations of mouse haematopoietic progenitor cells, spontaneous 'outlier' cells with either extremely high or low expression levels of the stem cell marker Sca-1 (also known as Ly6a; ref. 9) reconstitute the parental distribution of Sca-1 but do so only after more than one week. This slow relaxation is described by a gaussian mixture model that incorporates noise-driven transitions between discrete subpopulations, suggesting hidden multi-stability within one cell type. Despite clonality, the Sca-1 outliers had distinct transcriptomes. Although their unique gene expression profiles eventually reverted to that of the median cells, revealing an attractor state, they lasted long enough to confer a greatly different proclivity for choosing either the erythroid or the myeloid lineage. Preference in lineage choice was associated with increased expression of lineage-specific transcription factors, such as a >200-fold increase in Gata1 (ref. 10) among the erythroid-prone cells, or a >15-fold increased PU.1 (Sfpi1) (ref. 11) expression among myeloid-prone cells. Thus, clonal heterogeneity of gene expression level is not due to independent noise in the expression of individual genes, but reflects metastable states of a slowly fluctuating transcriptome that is distinct in individual cells and may govern the reversible, stochastic priming of multipotent progenitor cells in cell fate decision.
BibTeX: @article{ChaHemBar08, author = {Chang, Hannah H and Hemberg, Martin and Barahona, Mauricio and Ingber, Donald E and Huang, Sui}, title = {Transcriptome-wide noise controls lineage choice in mammalian progenitor cells}, journal = {Nature}, year = {2008}, volume = {453}, number = {7194}, pages = {544--7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18497826}, doi = {http://dx.doi.org/10.1038/nature06965} }
ChaPalKin07	Chang, J.T.; Palanivel, V.R.; Kinjyo, I.; Schambach, F.; Intlekofer, A.M.; Banerjee, A.; Longworth, S. a.; Vinup, K.E.; Mrass, P.; Oliaro, J.; Killeen, N.; Orange, J.S.; Russell, S.M.; Weninger, W. & Reiner, S.L.	Asymmetric T lymphocyte division in the initiation of adaptive immune responses [Abstract] [BibTeX] [URL] [PDF]	2007	Science Vol. 315 (5819) , pp. 1687-91	article	metabolic, signalling
Abstract: A hallmark of mammalian immunity is the heterogeneity of cell fate that exists among pathogen-experienced lymphocytes. We show that a dividing T lymphocyte initially responding to a microbe exhibits unequal partitioning of proteins that mediate signaling, cell fate specification, and asymmetric cell division. Asymmetric segregation of determinants appears to be coordinated by prolonged interaction between the T cell and its antigen-presenting cell before division. Additionally, the first two daughter T cells displayed phenotypic and functional indicators of being differentially fated toward effector and memory lineages. These results suggest a mechanism by which a single lymphocyte can apportion diverse cell fates necessary for adaptive immunity.
BibTeX: @article{ChaPalKin07, author = {Chang, John T and Palanivel, Vikram R and Kinjyo, Ichiko and Schambach, Felix and Intlekofer, Andrew M and Banerjee, Arnob and Longworth, Sarah a and Vinup, Kristine E and Mrass, Paul and Oliaro, Jane and Killeen, Nigel and Orange, Jordan S and Russell, Sarah M and Weninger, Wolfgang and Reiner, Steven L}, title = {Asymmetric T lymphocyte division in the initiation of adaptive immune responses}, journal = {Science}, year = {2007}, volume = {315}, number = {5819}, pages = {1687--91}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17332376}, doi = {http://dx.doi.org/10.1126/science.1139393} }
ChaBreWat04	Charbon, G.; Breunig, K.D.; Wattiez, R.; Vandenhaute, J. & Noël-Georis, I.	Key role of Ser562/661 in Snf1-dependent regulation of Cat8p in Saccharomyces cerevisiae and Kluyveromyces lactis [BibTeX] [PDF]	2004	Mol. Cell. Biol. Vol. 24 (10) , pp. 4083-4091	article	signalling
BibTeX: @article{ChaBreWat04, author = {Charbon, Godefroid and Breunig, Karin D and Wattiez, Ruddy and Vandenhaute, Jean and Noël-Georis, Isabelle}, title = {Key role of Ser562/661 in Snf1-dependent regulation of Cat8p in Saccharomyces cerevisiae and Kluyveromyces lactis}, journal = {Mol. Cell. Biol.}, year = {2004}, volume = {24}, number = {10}, pages = {4083--4091}, doi = {http://dx.doi.org/10.1128/MCB.24.10.4083} }
CloChrAgg08	Cloos, P. a.C.; Christensen, J.; Agger, K. & Helin, K.	Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease [Abstract] [BibTeX] [URL] [PDF]	2008	Gene. Dev. Vol. 22 (9) , pp. 1115-40	article	histone
Abstract: The enzymes catalyzing lysine and arginine methylation of histones are essential for maintaining transcriptional programs and determining cell fate and identity. Until recently, histone methylation was regarded irreversible. However, within the last few years, several families of histone demethylases erasing methyl marks associated with gene repression or activation have been identified, underscoring the plasticity and dynamic nature of histone methylation. Recent discoveries have revealed that histone demethylases take part in large multiprotein complexes synergizing with histone deacetylases, histone methyltransferases, and nuclear receptors to control developmental and transcriptional programs. Here we review the emerging biochemical and biological functions of the histone demethylases and discuss their potential involvement in human diseases, including cancer.
BibTeX: @article{CloChrAgg08, author = {Cloos, Paul a C and Christensen, Jesper and Agger, Karl and Helin, Kristian}, title = {Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease}, journal = {Gene. Dev.}, year = {2008}, volume = {22}, number = {9}, pages = {1115--40}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2732404&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1101/gad.1652908} }
CohGevEde08	Cohen, a. a.; Geva-Zatorsky, N.; Eden, E.; Frenkel-Morgenstern, M.; Issaeva, I.; Sigal, a.; Milo, R.; Cohen-Saidon, C.; Liron, Y.; Kam, Z.; Cohen, L.; Danon, T.; Perzov, N. & Alon, U.	Dynamic proteomics of individual cancer cells in response to a drug [Abstract] [BibTeX] [URL] [PDF]	2008	Science Vol. 322 (5907) , pp. 1511-6	article	metabolic, signalling
Abstract: Why do seemingly identical cells respond differently to a drug? To address this, we studied the dynamics and variability of the protein response of human cancer cells to a chemotherapy drug, camptothecin. We present a dynamic-proteomics approach that measures the levels and locations of nearly 1000 different endogenously tagged proteins in individual living cells at high temporal resolution. All cells show rapid translocation of proteins specific to the drug mechanism, including the drug target (topoisomerase-1), and slower, wide-ranging temporal waves of protein degradation and accumulation. However, the cells differ in the behavior of a subset of proteins. We identify proteins whose dynamics differ widely between cells, in a way that corresponds to the outcomes-cell death or survival. This opens the way to understanding molecular responses to drugs in individual cells.
BibTeX: @article{CohGevEde08, author = {Cohen, a a and Geva-Zatorsky, N and Eden, E and Frenkel-Morgenstern, M and Issaeva, I and Sigal, a and Milo, R and Cohen-Saidon, C and Liron, Y and Kam, Z and Cohen, L and Danon, T and Perzov, N and Alon, U}, title = {Dynamic proteomics of individual cancer cells in response to a drug}, journal = {Science}, year = {2008}, volume = {322}, number = {5907}, pages = {1511--6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19023046}, doi = {http://dx.doi.org/10.1126/science.1160165} }
Coh05	Cohn, M.	Degeneracy, mimicry and crossreactivity in immune recognition [Abstract] [BibTeX] [URL] [PDF]	2005	Mol. Immunol. Vol. 42 (5) , pp. 651-5	article	metabolic, signalling
Abstract: Degeneracy of recognition of antigen by the immune system is being used as an argument that the self-nonself discrimination cannot be a property of the specificity of its antigen-receptors, TCR and BCR, but must rely on emergent properties derived from a set of complex interactions and pathways. This essay analyzes an alternative view by showing that degeneracy and specificity are not mutually exclusive properties. The self-nonself discrimination is the sole evolutionary selection pressure for the specificity of the TCR and BCR, which can be quantitated as a "Specificity Index." Degeneracy is a non-issue for the self-nonself discrimination largely because it is a problem of chemistry, not of biology.
BibTeX: @article{Coh05, author = {Cohn, Melvin}, title = {Degeneracy, mimicry and crossreactivity in immune recognition}, journal = {Mol. Immunol.}, year = {2005}, volume = {42}, number = {5}, pages = {651--5}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15607824}, doi = {http://dx.doi.org/10.1016/j.molimm.2004.09.010} }
Col09	Coleman, A.W.	Is there a molecular key to the level of ``biological species'' in eukaryotes? A DNA guide [Abstract] [BibTeX] [URL] [PDF]	2009	Mol. Phylogenet. Evol. Vol. 50 (1) , pp. 197-203	article	genetic
Abstract: DNA sequences, powerful for phylogeny, have not yet proven as rewarding for taxonomic categorization purposes. However, further analyses of one locus, the second Internal Transcribed Spacer of the nuclear ribosomal gene cistron, has suggested a high degree of predictability across eukaryotes. Comparison of the secondary structure of ITS2 transcripts reveals its most conserved region, on the 5'-side of helix III. Comparison of this 5' 30 bp highly conserved region with the extent of sexual compatibility in a clade of organisms produces two useful predictions: identity of this region predicts meaningful intercrossing ability, and, difference of even one CBC pairing in this region predicts total failure of crossing. Previous to the appearance of the first CBC in the highly conserved portion, all gametic compatibility has been lost, thanks to the parallel evolutionary changes in genes controlling mating. These two landmark events help to delimit the level of interbreeding taxa.
BibTeX: @article{Col09, author = {Coleman, Annette W}, title = {Is there a molecular key to the level of ``biological species'' in eukaryotes? A DNA guide}, journal = {Mol. Phylogenet. Evol.}, publisher = {Elsevier Inc.}, year = {2009}, volume = {50}, number = {1}, pages = {197--203}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18992828}, doi = {http://dx.doi.org/10.1016/j.ympev.2008.10.008} }
CosWol05	Cosgrove, M. & Wolberger, C.	How does the histone code work? [BibTeX] [PDF]	2005	Biochemistry and cell biology Vol. 83 (4) , pp. 468-476	article
BibTeX: @article{CosWol05, author = {Cosgrove, M.S. and Wolberger, C.}, title = {How does the histone code work?}, journal = {Biochemistry and cell biology}, publisher = {NRC Research Press}, year = {2005}, volume = {83}, number = {4}, pages = {468--476} }
CriBreKlu76	Crick, F.; Brenner, S.; Klug, A. & Pieczenik, G.	A speculation on the origin of protein synthesis [BibTeX] [PDF]	1976	Orig. Life Vol. 7 , pp. 389-397	article	genetic
BibTeX: @article{CriBreKlu76, author = {Crick, F.H.C and Brenner, S and Klug, A and Pieczenik, G}, title = {A speculation on the origin of protein synthesis}, journal = {Orig. Life}, year = {1976}, volume = {7}, pages = {389--397} }
CruLoiS05	de la Cruz, X.; Lois, S.; Sánchez-Molina, S. & Martnez-Balbás, M. a.	Do protein motifs read the histone code? [Abstract] [BibTeX] [URL] [PDF]	2005	BioEssays Vol. 27 (2) , pp. 164-75	article	histone
Abstract: The existence of different patterns of chemical modifications (acetylation, methylation, phosphorylation, ubiquitination and ADP-ribosylation) of the histone tails led, some years ago, to the histone code hypothesis. According to this hypothesis, these modifications would provide binding sites for proteins that can change the chromatin state to either active or repressed. Interestingly, some protein domains present in histone-modifying enzymes are known to interact with these covalent marks in the histone tails. This was first shown for the bromodomain, which was found to interact selectively with acetylated lysines at the histone tails. More recently, it has been described that the chromodomain can be targeted to methylation marks in histone N-terminal domains. Finally, the interaction between the SANT domain and histones is also well documented. Overall, experimental evidence suggests that these domains could be involved in the recruitment of histone-modifying enzymes to discrete chromosomal locations, and/or in the regulation their enzymatic activity. Within this context, we review the distribution of bromodomains, chromodomains and SANT domains among chromatin-modifying enzymes and discuss how they can contribute to the translation of the histone code.
BibTeX: @article{CruLoiS05, author = {de la Cruz, Xavier and Lois, Sergio and Sánchez-Molina, Sara and Martnez-Balbás, Marian a}, title = {Do protein motifs read the histone code?}, journal = {BioEssays}, year = {2005}, volume = {27}, number = {2}, pages = {164--75}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15666348}, doi = {http://dx.doi.org/10.1002/bies.20176} }
DasTicBre05	Dasen, J.S.; Tice, B.C.; Brenner-Morton, S. & Jessell, T.M.	A Hox regulatory network establishes motor neuron pool identity and target-muscle connectivity [Abstract] [BibTeX] [URL] [PDF]	2005	Cell Vol. 123 (3) , pp. 477-91	article	neural
Abstract: Spinal motor neurons acquire specialized "pool" identities that determine their ability to form selective connections with target muscles in the limb, but the molecular basis of this striking example of neuronal specificity has remained unclear. We show here that a Hox transcriptional regulatory network specifies motor neuron pool identity and connectivity. Two interdependent sets of Hox regulatory interactions operate within motor neurons, one assigning rostrocaudal motor pool position and a second directing motor pool diversity at a single segmental level. This Hox regulatory network directs the downstream transcriptional identity of motor neuron pools and defines the pattern of target-muscle connectivity.
BibTeX: @article{DasTicBre05, author = {Dasen, Jeremy S and Tice, Bonnie C and Brenner-Morton, Susan and Jessell, Thomas M}, title = {A Hox regulatory network establishes motor neuron pool identity and target-muscle connectivity}, journal = {Cell}, year = {2005}, volume = {123}, number = {3}, pages = {477--91}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16269338}, doi = {http://dx.doi.org/10.1016/j.cell.2005.09.009} }
DavBruKat06	Davis, E.E.; Brueckner, M. & Katsanis, N.	The emerging complexity of the vertebrate cilium: new functional roles for an ancient organelle [Abstract] [BibTeX] [URL] [PDF]	2006	Dev. Cell Vol. 11 (1) , pp. 9-19	article	embryology, developmental
Abstract: Cilia and flagella are found on the surface of a strikingly diverse range of cell types. These intriguing organelles, with their unique and highly adapted protein transport machinery, have been studied extensively in the context of cellular locomotion, sexual reproduction, or fluid propulsion. However, recent studies are beginning to show that in vertebrates particularly, cilia have been recruited to perform additional developmental and homeostatic roles. Here, we review advances in deciphering the functional components of cilia, and we explore emerging trends that implicate ciliary proteins in signal transduction and morphogenetic pathways.
BibTeX: @article{DavBruKat06, author = {Davis, Erica E and Brueckner, Martina and Katsanis, Nicholas}, title = {The emerging complexity of the vertebrate cilium: new functional roles for an ancient organelle}, journal = {Dev. Cell}, year = {2006}, volume = {11}, number = {1}, pages = {9--19}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16824949}, doi = {http://dx.doi.org/10.1016/j.devcel.2006.06.009} }
DeuMeiKup06	Deutscher, D.; Meilijson, I.; Kupiec, M. & Ruppin, E.	Multiple knockout analysis of genetic robustness in the yeast metabolic network [Abstract] [BibTeX] [URL] [PDF]	2006	Nat. Genet. Vol. 38 (9) , pp. 993-8	article	metabolic, signalling
Abstract: Genetic robustness characterizes the constancy of the phenotype in face of heritable perturbations. Previous investigations have used comprehensive single and double gene knockouts to study gene essentiality and pairwise gene interactions in the yeast Saccharomyces cerevisiae. Here we conduct an in silico multiple knockout investigation of a flux balance analysis model of the yeast's metabolic network. Cataloging gene sets that provide mutual functional backup, we identify sets of up to eight interacting genes and characterize the 'k robustness' (the depth of backup interactions) of each gene. We find that 74% (360) of the metabolic genes participate in processes that are essential to growth in a standard laboratory environment, compared with only 13% previously found to be essential using single knockouts. The genes' k robustness is shown to be a solid indicator of their biological buffering capacity and is correlated with both the genes' environmental specificity and their evolutionary retention.
BibTeX: @article{DeuMeiKup06, author = {Deutscher, David and Meilijson, Isaac and Kupiec, Martin and Ruppin, Eytan}, title = {Multiple knockout analysis of genetic robustness in the yeast metabolic network}, journal = {Nat. Genet.}, year = {2006}, volume = {38}, number = {9}, pages = {993--8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16941010}, doi = {http://dx.doi.org/10.1038/ng1856} }
DeuMeiSch08	Deutscher, D.; Meilijson, I.; Schuster, S. & Ruppin, E.	Can single knockouts accurately single out gene functions? [Abstract] [BibTeX] [URL] [PDF]	2008	BMC Syst. Biol. Vol. 2 , pp. 50	article	genetic
Abstract: When analyzing complex biological systems, a major objective is localization of function - assessing how much each element contributes to the execution of specific tasks. To establish causal relationships, knockout and perturbation studies are commonly executed. The vast majority of studies perturb a single element at a time, yet one may hypothesize that in non-trivial biological systems single-perturbations will fail to reveal the functional organization of the system, owing to interactions and redundancies.
BibTeX: @article{DeuMeiSch08, author = {Deutscher, David and Meilijson, Isaac and Schuster, Stefan and Ruppin, Eytan}, title = {Can single knockouts accurately single out gene functions?}, journal = {BMC Syst. Biol.}, year = {2008}, volume = {2}, pages = {50}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2443110&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1186/1752-0509-2-50} }
DhiBurSan10	Dhir, A.; Buratti, E.; van Santen, M. a.; Lührmann, R. & Baralle, F.E.	The intronic splicing code: multiple factors involved in ATM pseudoexon definition [Abstract] [BibTeX] [URL] [PDF]	2010	EMBO J. Vol. 29 (4) , pp. 749-60	article	splicing
Abstract: Abundance of pseudo splice sites in introns can potentially give rise to innumerable pseudoexons, outnumbering the real ones. Nonetheless, these are efficiently ignored by the splicing machinery, a process yet to be understood completely. Although numerous 5' splice site-like sequences functioning as splicing silencers have been found to be enriched in predicted human pseudoexons, the lack of active pseudoexons pose a fundamental challenge to how these U1snRNP-binding sites function in splicing inhibition. Here, we address this issue by focusing on a previously described pathological ATM pseudoexon whose inhibition is mediated by U1snRNP binding at intronic splicing processing element (ISPE), composed of a consensus donor splice site. Spliceosomal complex assembly demonstrates inefficient A complex formation when ISPE is intact, implying U1snRNP-mediated unproductive U2snRNP recruitment. Furthermore, interaction of SF2/ASF with its motif seems to be dependent on RNA structure and U1snRNP interaction. Our results suggest a complex combinatorial interplay of RNA structure and trans-acting factors in determining the splicing outcome and contribute to understanding the intronic splicing code for the ATM pseudoexon.
BibTeX: @article{DhiBurSan10, author = {Dhir, Ashish and Buratti, Emanuele and van Santen, Maria a and Lührmann, Reinhard and Baralle, Francisco E}, title = {The intronic splicing code: multiple factors involved in ATM pseudoexon definition}, journal = {EMBO J.}, year = {2010}, volume = {29}, number = {4}, pages = {749--60}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2829169&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1038/emboj.2009.397} }
Di00	Di Lorenzo, P.M.	The neural code for taste in the brain stem: response profiles [Abstract] [BibTeX] [URL] [PDF]	2000	Physiology & behavior Vol. 69 (1-2) , pp. 87-96	article	brain transcription
Abstract: In the study of the neural code for taste, two theories have dominated the literature: the across neuron pattern (ANP), and the labeled line theories. Both of these theories are based on the observations that taste cells are multisensitive across a variety of different taste stimuli. Given a fixed array of taste stimuli, a cell's particular set of sensitivities defines its response profile. The characteristics of response profiles are the basis of both major theories of coding. In reviewing the literature, it is apparent that response profiles are an expression of a complex interplay of excitatory and inhibitory inputs that derive from cells with a wide variety of sensitivity patterns. These observations suggest that, in the absence of inhibition, taste cells might be potentially responsive to all taste stimuli. Several studies also suggest that response profiles can be influenced by the taste context, defined as the taste stimulus presented just before or simultaneously with another, under which they are recorded. A theory, called dynamic coding, was proposed to account for context dependency of taste response profiles. In this theory, those cells that are unaffected by taste context would provide the signal, i.e., the information-containing portion of the ANP, and those cells whose responses are context dependent would provide noise, i.e., less stimulus specific information. When singular taste stimuli are presented, noise cells would provide amplification of the signal, and when complex mixtures are presented, the responses of the noise cells would be suppressed (depending on the particular combination of tastants), and the ratio of signal to noise would be enhanced.
BibTeX: @article{Di00, author = {Di Lorenzo, P M}, title = {The neural code for taste in the brain stem: response profiles}, journal = {Physiology & behavior}, year = {2000}, volume = {69}, number = {1-2}, pages = {87--96}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10854920} }
DolDasWei07	Dolinoy, D.C.; Das, R.; Weidman, J.R. & Jirtle, R.L.	Metastable epialleles, imprinting, and the fetal origins of adult diseases [Abstract] [BibTeX] [URL] [PDF]	2007	Pediatr. Res. Vol. 61 (5 Pt 2) , pp. 30R-37R	article	epigenetic
Abstract: Epigenetics is the study of the heritable changes in gene expression that occur without a change in the DNA sequence itself. These heritable epigenetic changes include chromatin folding and attachment to the nuclear matrix, packaging of DNA around nucleosomes, histone modifications, and DNA methylation. The epigenome is particularly susceptible to dysregulation during gestation, neonatal development, puberty, and old age. Nevertheless, it is most vulnerable to environmental factors during embryogenesis because the DNA synthetic rate is high, and the elaborate DNA methylation patterning and chromatin structure required for normal tissue development is established during early development. Metastable epialleles are alleles that are variably expressed in genetically identical individuals due to epigenetic modifications established during early development and are thought to be particularly vulnerable to environmental influences. The viable yellow agouti (A(vy)) allele, whose expression is correlated to DNA methylation, is a murine metastable epiallele, which has been used as an epigenetic biosensor for environmental factors affecting the fetal epigenome. In this review, we introduce epigenetic gene regulation, describe important epigenetic phenomenon in mammals, summarize literature linking the early environment to developmental plasticity of the fetal epigenome, and promote the necessity to identify epigenetically labile genes in the mouse and human genomes.
BibTeX: @article{DolDasWei07, author = {Dolinoy, Dana C and Das, Radhika and Weidman, Jennifer R and Jirtle, Randy L}, title = {Metastable epialleles, imprinting, and the fetal origins of adult diseases}, journal = {Pediatr. Res.}, year = {2007}, volume = {61}, number = {5 Pt 2}, pages = {30R--37R}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17413847}, doi = {http://dx.doi.org/10.1203/pdr.0b013e31804575f7} }
Dou52	Dounce, A. & others	Duplicating mechanism for peptide chain and nucleic acid synthesis [BibTeX]	1952	Enzymologia Vol. 15 (5) , pp. 251	article	genetic
BibTeX: @article{Dou52, author = {Dounce, A.L. and others}, title = {Duplicating mechanism for peptide chain and nucleic acid synthesis}, journal = {Enzymologia}, year = {1952}, volume = {15}, number = {5}, pages = {251} }
Dov00	Dover, G.	How genomic and developmental dynamics affect evolutionary processes [Abstract] [BibTeX] [URL] [PDF]	2000	BioEssays Vol. 22 (12) , pp. 1153-9	article	genetic
Abstract: Evolutionary genetics is concerned with natural selection and neutral drift, to the virtual exclusion of almost everything else. In its current focus on DNA variation, it reduces phenotypes to symbols. Varying phenotypes, however, are the units of evolution, and, if we want a comprehensive theory of evolution, we need to consider both the internal and external evolutionary forces that shape the development of phenotypes. Genetic systems are redundant, modular and subject to a variety of genomic mechanisms of "turnover" (transposition, gene conversion, unequal crossingover, slippage and so on). As such the construction and spread of novel combinations of modules by turnover, in particular within gene promoters, contributes significantly to the evolution of phenotypes. Furthermore, redundancy, turnover and modularity lead to ever more complex networks of genetic interactions and ever more functions for a given module. The significant interaction between genomic turnover and natural selection leads to a molecular coevolution between interacting modules and hence facilitates the establishment of biological novelties.
BibTeX: @article{Dov00, author = {Dover, G}, title = {How genomic and developmental dynamics affect evolutionary processes}, journal = {BioEssays}, year = {2000}, volume = {22}, number = {12}, pages = {1153--9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11084631}, doi = {http://dx.doi.org/10.1002/1521-1878(200012)22:12<1153::AID-BIES13>3.0.CO;2-0} }
DunObr01	Dunker, a.K. & Obradovic, Z.	The protein trinity--linking function and disorder [BibTeX] [URL] [PDF]	2001	Nat. Biotechnol. Vol. 19 (9) , pp. 805-6	article	metabolic, signalling
BibTeX: @article{DunObr01, author = {Dunker, a K and Obradovic, Z}, title = {The protein trinity---linking function and disorder}, journal = {Nat. Biotechnol.}, year = {2001}, volume = {19}, number = {9}, pages = {805--6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11533628}, doi = {http://dx.doi.org/10.1038/nbt0901-805} }
Fei08	Feinberg, A.P.	Epigenetics at the epicenter of modern medicine [Abstract] [BibTeX] [URL] [PDF]	2008	J. Amer. Med. Assoc. Vol. 299 (11) , pp. 1345-50	article	epigenetic
Abstract: Epigenetics, the study of non-DNA sequence-related heredity, is at the epicenter of modern medicine because it can help to explain the relationship between an individual's genetic background, the environment, aging, and disease. It can do so because the epigenetic state varies among tissues and during a lifetime, whereas the DNA sequence remains essentially the same. As cells adapt to a changing internal and external environment, epigenetic mechanisms can remember these changes in the normal programming and reprogramming of gene activity. The common disease genetic and epigenetic (CDGE) model provides an epidemiologic framework that can incorporate epigenetic with genetic variation in the context of age-related susceptibility to disease. Under CDGE, the epigenetic program can modify the effects of deleterious genes or may be influenced by an adverse environment. Thus, including epigenetics into epidemiologic studies of human disease may help explain the relationship between the genome and the environment and may provide new clues to modifying these effects in disease prevention and therapy.
BibTeX: @article{Fei08, author = {Feinberg, Andrew P}, title = {Epigenetics at the epicenter of modern medicine}, journal = {J. Amer. Med. Assoc.}, year = {2008}, volume = {299}, number = {11}, pages = {1345--50}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18349095}, doi = {http://dx.doi.org/10.1001/jama.299.11.1345} }
Fei07	Feinberg, A.P.	Phenotypic plasticity and the epigenetics of human disease [Abstract] [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 433-40	article	epigenetic
Abstract: It is becoming clear that epigenetic changes are involved in human disease as well as during normal development. A unifying theme of disease epigenetics is defects in phenotypic plasticity--cells' ability to change their behaviour in response to internal or external environmental cues. This model proposes that hereditary disorders of the epigenetic apparatus lead to developmental defects, that cancer epigenetics involves disruption of the stem-cell programme, and that common diseases with late-onset phenotypes involve interactions between the epigenome, the genome and the environment. Increased understanding of epigenetic-disease mechanisms could lead to disease-risk stratification for targeted intervention and to targeted therapies.
BibTeX: @article{Fei07, author = {Feinberg, Andrew P}, title = {Phenotypic plasticity and the epigenetics of human disease}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {433--40}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17522677}, doi = {http://dx.doi.org/10.1038/nature05919} }
FlaPlaGel07	Flames, N.; Pla, R.; Gelman, D.M.; Rubenstein, J.L.R.; Puelles, L. & Marn, O.	Delineation of multiple subpallial progenitor domains by the combinatorial expression of transcriptional codes [Abstract] [BibTeX] [URL] [PDF]	2007	J. Neurosci. Vol. 27 (36) , pp. 9682-95	article	brain transcription
Abstract: The mammalian telencephalon is considered the most complex of all biological structures. It comprises a large number of functionally and morphologically distinct types of neurons that coordinately control most aspects of cognition and behavior. The subpallium, for example, not only gives rise to multiple neuronal types that form the basal ganglia and parts of the amygdala and septum but also is the origin of an astonishing diversity of cortical interneurons. Despite our detailed knowledge on the molecular, morphological, and physiological properties of most of these neuronal populations, the mechanisms underlying their generation are still poorly understood. Here, we comprehensively analyzed the expression patterns of several transcription factors in the ventricular zone of the developing subpallium in the mouse to generate a detailed molecular map of the different progenitor domains present in this region. Our study demonstrates that the ventricular zone of the mouse subpallium contains at least 18 domains that are uniquely defined by the combinatorial expression of several transcription factors. Furthermore, the results of microtransplantation experiments in vivo corroborate that anatomically defined regions of the mouse subpallium, such as the medial ganglionic eminence, can be subdivided into functionally distinct domains.
BibTeX: @article{FlaPlaGel07, author = {Flames, Nuria and Pla, Ramón and Gelman, Diego M and Rubenstein, John L R and Puelles, Luis and Marn, Oscar}, title = {Delineation of multiple subpallial progenitor domains by the combinatorial expression of transcriptional codes}, journal = {J. Neurosci.}, year = {2007}, volume = {27}, number = {36}, pages = {9682--95}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17804629}, doi = {http://dx.doi.org/10.1523/JNEUROSCI.2750-07.2007} }
FonGar04	Fondon, J.W. & Garner, H.R.	Molecular origins of rapid and continuous morphological evolution [Abstract] [BibTeX] [URL] [PDF]	2004	Proc. Natl. Acad. Sci. U.S.A. Vol. 101 (52) , pp. 18058-63	article	embryology, developmental
Abstract: Mutations in cis-regulatory sequences have been implicated as being the predominant source of variation in morphological evolution. We offer a hypothesis that gene-associated tandem repeat expansions and contractions are a major source of phenotypic variation in evolution. Here, we describe a comparative genomic study of repetitive elements in developmental genes of 92 breeds of dogs. We find evidence for selection for divergence at coding repeat loci in the form of both elevated purity and extensive length polymorphism among different breeds. Variations in the number of repeats in the coding regions of the Alx-4 (aristaless-like 4) and Runx-2 (runt-related transcription factor 2) genes were quantitatively associated with significant differences in limb and skull morphology. We identified similar repeat length variation in the coding repeats of Runx-2, Twist, and Dlx-2 in several other species. The high frequency and incremental effects of repeat length mutations provide molecular explanations for swift, yet topologically conservative morphological evolution.
BibTeX: @article{FonGar04, author = {Fondon, John W and Garner, Harold R}, title = {Molecular origins of rapid and continuous morphological evolution}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2004}, volume = {101}, number = {52}, pages = {18058--63}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=539791&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1073/pnas.0408118101} }
FraBic07	Fraser, P. & Bickmore, W.	Nuclear organization of the genome and the potential for gene regulation [Abstract] [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 413-7	article	epigenetic
Abstract: Much work has been published on the cis-regulatory elements that affect gene function locally, as well as on the biochemistry of the transcription factors and chromatin- and histone-modifying complexes that influence gene expression. However, surprisingly little information is available about how these components are organized within the three-dimensional space of the nucleus. Technological advances are now helping to identify the spatial relationships and interactions of genes and regulatory elements in the nucleus and are revealing an unexpectedly extensive network of communication within and between chromosomes. A crucial unresolved issue is the extent to which this organization affects gene function, rather than just reflecting it.
BibTeX: @article{FraBic07, author = {Fraser, Peter and Bickmore, Wendy}, title = {Nuclear organization of the genome and the potential for gene regulation}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {413--7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17522674}, doi = {http://dx.doi.org/10.1038/nature05916} }
Gam54	Gamow, G.	Possible relation between deoxyribonucleic acid and protein structures [BibTeX]	1954	Nature Vol. 173 , pp. 318	article	genetic
BibTeX: @article{Gam54, author = {Gamow, G.}, title = {Possible relation between deoxyribonucleic acid and protein structures}, journal = {Nature}, publisher = {Nature Publishing Group}, year = {1954}, volume = {173}, pages = {318} }
Gar68	Garen, A.	Sense and nonsense in the genetic code [BibTeX] [PDF]	1968	Science Vol. 160 (3824) , pp. 149-159	article	genetic
BibTeX: @article{Gar68, author = {Garen, Alan}, title = {Sense and nonsense in the genetic code}, journal = {Science}, year = {1968}, volume = {160}, number = {3824}, pages = {149--159} }
GrMan08	Gräff, J. & Mansuy, I.M.	Epigenetic codes in cognition and behaviour [Abstract] [BibTeX] [URL] [PDF]	2008	Behav. Brain Res. Vol. 192 (1) , pp. 70-87	article	histone
Abstract: The epigenetic marking of chromatin provides a ubiquitous means for cells to shape and maintain their identity, and to react to environmental stimuli via specific remodeling. Such an epigenetic code of the core components of chromatin, DNA and histone proteins, can thus be stable but is also highly dynamic. In the nervous system, epigenetic codes are critical for basic cellular processes such as synaptic plasticity, and for complex behaviours such as learning and memory. At the same time, epigenetic marks can be stably transmitted through mitosis and meiosis, and thereby underlie non-genomic transgenerational inheritance of behavioural traits. In this review, we describe recent findings on the role and mechanisms of epigenetic codes in the brain, and discuss their implication in synaptic plasticity, cognitive functions and psychiatric disorders. We provide examples of transgenerational inheritance of epigenetic marks that affect simple morphological traits or complex processes such as disease susceptibility, and point to the potential implication of epigenetic codes in medicine and evolution.
BibTeX: @article{GrMan08, author = {Gräff, Johannes and Mansuy, Isabelle M}, title = {Epigenetic codes in cognition and behaviour}, journal = {Behav. Brain Res.}, year = {2008}, volume = {192}, number = {1}, pages = {70--87}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18353453}, doi = {http://dx.doi.org/10.1016/j.bbr.2008.01.021} }
GreElg07	Grewal, S.I.S. & Elgin, S.C.R.	Transcription and RNA interference in the formation of heterochromatin [Abstract] [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 399-406	article	epigenetic
Abstract: Transcription in heterochromatin seems to be an oxymoron--surely the 'silenced' form of chromatin should not be transcribed. But there have been frequent reports of low-level transcription in heterochromatic regions, and several hundred genes are found in these regions in Drosophila. Most strikingly, recent investigations implicate RNA interference mechanisms in targeting and maintaining heterochromatin, and these mechanisms are inherently dependent on transcription. Silencing of chromatin might involve trans-acting sources of the crucial small RNAs that carry out RNA interference, but in some cases, transcription of the region to be silenced seems to be required--an apparent contradiction.
BibTeX: @article{GreElg07, author = {Grewal, Shiv I S and Elgin, Sarah C R}, title = {Transcription and RNA interference in the formation of heterochromatin}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {399--406}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2950806&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1038/nature05914} }
GudPhiLen06	Guder, C.; Philipp, I.; Lengfeld, T.; Watanabe, H.; Hobmayer, B. & Holstein, T.W.	The Wnt code: cnidarians signal the way [Abstract] [BibTeX] [URL] [PDF]	2006	Oncogene Vol. 25 (57) , pp. 7450-60	article	embryology, developmental
Abstract: Cnidarians are the simplest metazoans with a nervous system. They are well known for their regeneration capacity, which is based on the restoration of a signalling centre (organizer). Recent work has identified the canonical Wnt pathway in the freshwater polyp Hydra, where it acts in organizer formation and regeneration. Wnt signalling is also essential for cnidarian embryogenesis. In the sea anemone Nematostella vectensis 11 of the 12 known wnt gene subfamilies were identified. Different wnt genes exhibit serial and overlapping expression domains along the oral-aboral axis of the embryo (the 'wnt code'). This is reminiscent of the hox code (cluster) in bilaterian embryogenesis that is, however, absent in cnidarians. It is proposed that the common ancestor of cnidarians and bilaterians invented a set of wnt genes that patterned the ancient main body axis. Major antagonists of Wnt ligands (e.g. Dkk 1/2/4) that were previously known only from chordates, are also present in cnidarians and exhibit a similar conserved function. The unexpectedly high level of genetic complexity of wnt genes evolved in early multi-cellular animals about 650 Myr ago and suggests a radical expansion of the genetic repertoire, concurrent with the evolution of multi-cellularity and the diversification of eumetazoan body plans.
BibTeX: @article{GudPhiLen06, author = {Guder, C and Philipp, I and Lengfeld, T and Watanabe, H and Hobmayer, B and Holstein, T W}, title = {The Wnt code: cnidarians signal the way}, journal = {Oncogene}, year = {2006}, volume = {25}, number = {57}, pages = {7450--60}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17143289}, doi = {http://dx.doi.org/10.1038/sj.onc.1210052} }
HalDi06	Hallock, R.M. & Di Lorenzo, P.M.	Temporal coding in the gustatory system [Abstract] [BibTeX] [URL] [PDF]	2006	Neurosci. Biobehav. Rev. Vol. 30 (8) , pp. 1145-60	article	neural
Abstract: Early investigations of temporal coding in the gustatory system showed that the time course of responses in some neurons showed systematic differences across the various classes of taste stimuli, implying that the temporal characteristics of a response can convey information about a taste stimulus. Studies of temporal coding in the gustatory system have grappled with several unique methodological challenges, including the quantitative description and comparison of temporal patterns as well as the assessment of the relative contributions of spatial and temporal coding to the information contained in a response to a tastant. Other investigations have suggested that the cooperative activity among synchronously firing ensembles of taste-responsive neurons at all levels of processing in the brain can convey information about taste quality (sweet, sour, salty, bitter and umami). Behavioral studies using patterned electrical stimulation of the brain in awake animals have supported the idea that temporal coding of taste stimuli may have functional significance.
BibTeX: @article{HalDi06, author = {Hallock, Robert M and Di Lorenzo, Patricia M}, title = {Temporal coding in the gustatory system}, journal = {Neurosci. Biobehav. Rev.}, year = {2006}, volume = {30}, number = {8}, pages = {1145--60}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16979239}, doi = {http://dx.doi.org/10.1016/j.neubiorev.2006.07.005} }
HenJac07	Henderson, I.R. & Jacobsen, S.E.	Epigenetic inheritance in plants [Abstract] [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 418-24	article	epigenetic
Abstract: The function of plant genomes depends on chromatin marks such as the methylation of DNA and the post-translational modification of histones. Techniques for studying model plants such as Arabidopsis thaliana have enabled researchers to begin to uncover the pathways that establish and maintain chromatin modifications, and genomic studies are allowing the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs seem to be important in determining the distribution of chromatin modifications, and RNA might also underlie the complex epigenetic interactions that occur between homologous sequences. Plants use these epigenetic silencing mechanisms extensively to control development and parent-of-origin imprinted gene expression.
BibTeX: @article{HenJac07, author = {Henderson, Ian R and Jacobsen, Steven E}, title = {Epigenetic inheritance in plants}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {418--24}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17522675}, doi = {http://dx.doi.org/10.1038/nature05917} }
HurKanLak07	Hurlbut, G.D.; Kankel, M.W.; Lake, R.J. & Artavanis-Tsakonas, S.	Crossing paths with Notch in the hyper-network [Abstract] [BibTeX] [URL] [PDF]	2007	Curr. Opin. Cell Biol. Vol. 19 (2) , pp. 166-75	article	signalling
Abstract: The development of complex and diverse metazoan morphologies is coordinated by a surprisingly small number of evolutionarily conserved signaling mechanisms. These signals can act in parallel but often appear to function as an integrated hyper-network. The nodes defining this complex molecular circuitry are poorly understood, but the biological significance of pathway cross-talk is profound. The importance of such large-scale signal integration is exemplified by Notch and its ability to cross-talk with all the major pathways to influence cell differentiation, proliferation, survival and migration. The Notch pathway is, thus, a useful paradigm to illustrate the complexity of pathway cross-talk: its pervasiveness, context dependency, and importance in development and disease.
BibTeX: @article{HurKanLak07, author = {Hurlbut, Gregory D and Kankel, Mark W and Lake, Robert J and Artavanis-Tsakonas, Spyros}, title = {Crossing paths with Notch in the hyper-network}, journal = {Curr. Opin. Cell Biol.}, year = {2007}, volume = {19}, number = {2}, pages = {166--75}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17317139}, doi = {http://dx.doi.org/10.1016/j.ceb.2007.02.012} }
JenAll01	Jenuwein, T. & Allis, C.	Translating the histone code [BibTeX] [PDF]	2001	Sci. STKE Vol. 293 (5532) , pp. 1074	article	histone
BibTeX: @article{JenAll01, author = {Jenuwein, T. and Allis, C.D.}, title = {Translating the histone code}, journal = {Sci. STKE}, publisher = {AAAS}, year = {2001}, volume = {293}, number = {5532}, pages = {1074} }
Jes00	Jessell, T.M.	Neuronal specification in the spinal cord: inductive signals and transcriptional codes [Abstract] [BibTeX] [URL] [PDF]	2000	Nat. Rev. Genet. Vol. 1 (1) , pp. 20-9	article	neural
Abstract: Neural circuits are assembled with remarkable precision during embryonic development, and the selectivity inherent in their formation helps to define the behavioural repertoire of the mature organism. In the vertebrate central nervous system, this developmental program begins with the differentiation of distinct classes of neurons from progenitor cells located at defined positions within the neural tube. The mechanisms that specify the identity of neural cells have been examined in many regions of the nervous system and reveal a high degree of conservation in the specification of cell fate by key signalling molecules.
BibTeX: @article{Jes00, author = {Jessell, T M}, title = {Neuronal specification in the spinal cord: inductive signals and transcriptional codes}, journal = {Nat. Rev. Genet.}, year = {2000}, volume = {1}, number = {1}, pages = {20--9}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11262869}, doi = {http://dx.doi.org/10.1038/35049541} }
JonYazMid04	Jones, L.S.; Yazzie, B. & Middaugh, C.R.	Polyanions and the proteome [Abstract] [BibTeX] [URL] [PDF]	2004	Mol. Cell Proteomics Vol. 3 (8) , pp. 746-69	article	metabolic, signalling
Abstract: The behavior of the proteome reflects spatial and temporal organization both within and without cells. We propose that various macromolecular entities possessing polyanionic character such as proteoglycans, lipid bilayer surfaces, microtubules, microfilaments, and polynucleotides may provide a functional network that mediates a variety of cellular phenomena. The interaction of proteins with this array of polyanions is characterized by a lower degree of specificity than seen with most commonly recognized macromolecular interactions. In this commentary, potential roles for this polyanion network in diverse functions such as protein/protein interactions, protein folding and stabilization, macromolecular transport, and various disease processes are all considered, as well as the use of polyanions as therapeutic agents. The role of small polyanions in the regulation of protein/polyanion interactions is also postulated. We provide preliminary experimental analysis of the extent to which proteins interact with polyanions inside cells using a combination of two-dimensional chromatographic and electrophoretic methods and antibody arrays. We conclude that many hundreds to thousands of such interactions are present in cells and argue that future understanding of the proteome will require that the "polyanion world" be taken into account.
BibTeX: @article{JonYazMid04, author = {Jones, LaToya S and Yazzie, Brian and Middaugh, C Russell}, title = {Polyanions and the proteome}, journal = {Mol. Cell Proteomics}, year = {2004}, volume = {3}, number = {8}, pages = {746--69}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15143156}, doi = {http://dx.doi.org/10.1074/mcp.R400008-MCP200} }
KaeElsBla05	Kaern, M.; Elston, T.C.; Blake, W.J. & Collins, J.J.	Stochasticity in gene expression: from theories to phenotypes [Abstract] [BibTeX] [URL] [PDF]	2005	Nat. Rev. Genet. Vol. 6 (6) , pp. 451-64	article	genetic
Abstract: Genetically identical cells exposed to the same environmental conditions can show significant variation in molecular content and marked differences in phenotypic characteristics. This variability is linked to stochasticity in gene expression, which is generally viewed as having detrimental effects on cellular function with potential implications for disease. However, stochasticity in gene expression can also be advantageous. It can provide the flexibility needed by cells to adapt to fluctuating environments or respond to sudden stresses, and a mechanism by which population heterogeneity can be established during cellular differentiation and development.
BibTeX: @article{KaeElsBla05, author = {Kaern, Mads and Elston, Timothy C and Blake, William J and Collins, James J}, title = {Stochasticity in gene expression: from theories to phenotypes}, journal = {Nat. Rev. Genet.}, year = {2005}, volume = {6}, number = {6}, pages = {451--64}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15883588}, doi = {http://dx.doi.org/10.1038/nrg1615} }
Kar08	Karsenti, E.	Self-organization in cell biology: a brief history [BibTeX] [PDF]	2008	Nat. Rev. Mol. Cell Biol. Vol. 9 , pp. 255-262	article	cytoskeletal
BibTeX: @article{Kar08, author = {Karsenti, Eric}, title = {Self-organization in cell biology: a brief history}, journal = {Nat. Rev. Mol. Cell Biol.}, year = {2008}, volume = {9}, pages = {255--262} }
KhiHsi04	Khidekel, N. & Hsieh-Wilson, L.C.	A `molecular switchboard'--covalent modifications to proteins and their impact on transcription [Abstract] [BibTeX] [URL] [PDF]	2004	Org. Biomol. Chem. Vol. 2 (1) , pp. 1-7	article	metabolic, signalling
Abstract: Proteins undergo a remarkable variety of posttranslational modifications, with more than 200 distinct modifications identified to date. Increasing evidence suggests that many proteins bear multiple, distinct modifications, and the ability of one modification to antagonize or synergize the deposition of another can have significant biological consequences. Here, we illustrate the importance of posttranslational modifications within the context of transcriptional regulation, and we offer a perspective on the emerging role of combinatorial networks of modifications. Finally, we discuss the potential for chemical approaches to transform our understanding of the field.
BibTeX: @article{KhiHsi04, author = {Khidekel, Nelly and Hsieh-Wilson, Linda C}, title = {A `molecular switchboard'---covalent modifications to proteins and their impact on transcription}, journal = {Org. Biomol. Chem.}, year = {2004}, volume = {2}, number = {1}, pages = {1--7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14737652}, doi = {http://dx.doi.org/10.1039/b312466e} }
KhoBGho66	Khorana, H.; Büuchi, H.; Ghosh, H.; Gupta, N.; Jacob, T.; Kössel, H.; Morgan, R.; Narang, S.; Ohtsuka, E. & Wells, R. Cold Spring Harbor Laboratory Press	Polynucleotide synthesis and the genetic code [BibTeX]	1966	Vol. 31 Cold Spring Harbor symposia on quantitative biology , pp. 39-49	inproceedings	genetic
BibTeX: @inproceedings{KhoBGho66, author = {Khorana, H.G. and Büuchi, H. and Ghosh, H. and Gupta, N. and Jacob, TM and Kössel, H. and Morgan, R. and Narang, SA and Ohtsuka, E. and Wells, RD}, title = {Polynucleotide synthesis and the genetic code}, booktitle = {Cold Spring Harbor symposia on quantitative biology}, year = {1966}, volume = {31}, pages = {39--49} }
KniCatDi06	Knights, C.D.; Catania, J.; Di Giovanni, S.; Muratoglu, S.; Perez, R.; Swartzbeck, A.; Quong, A. a.; Zhang, X.; Beerman, T.; Pestell, R.G. & Avantaggiati, M.L.	Distinct p53 acetylation cassettes differentially influence gene-expression patterns and cell fate [Abstract] [BibTeX] [URL] [PDF]	2006	J. Cell Biol. Vol. 173 (4) , pp. 533-44	article	acetylation
Abstract: The activity of the p53 gene product is regulated by a plethora of posttranslational modifications. An open question is whether such posttranslational changes act redundantly or dependently upon one another. We show that a functional interference between specific acetylated and phosphorylated residues of p53 influences cell fate. Acetylation of lysine 320 (K320) prevents phosphorylation of crucial serines in the NH(2)-terminal region of p53; only allows activation of genes containing high-affinity p53 binding sites, such as p21/WAF; and promotes cell survival after DNA damage. In contrast, acetylation of K373 leads to hyperphosphorylation of p53 NH(2)-terminal residues and enhances the interaction with promoters for which p53 possesses low DNA binding affinity, such as those contained in proapoptotic genes, leading to cell death. Further, acetylation of each of these two lysine clusters differentially regulates the interaction of p53 with coactivators and corepressors and produces distinct gene-expression profiles. By analogy with the "histone code" hypothesis, we propose that the multiple biological activities of p53 are orchestrated and deciphered by different "p53 cassettes," each containing combination patterns of posttranslational modifications and protein-protein interactions.
BibTeX: @article{KniCatDi06, author = {Knights, Chad D and Catania, Jason and Di Giovanni, Simone and Muratoglu, Selen and Perez, Ricardo and Swartzbeck, Amber and Quong, Andrew a and Zhang, Xiaojing and Beerman, Terry and Pestell, Richard G and Avantaggiati, Maria Laura}, title = {Distinct p53 acetylation cassettes differentially influence gene-expression patterns and cell fate}, journal = {J. Cell Biol.}, year = {2006}, volume = {173}, number = {4}, pages = {533--44}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2063863&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1083/jcb.200512059} }
KomRap12	Komander, D. & Rape, M.	The ubiquitin code [Abstract] [BibTeX] [URL] [PDF]	2012	Annu. Rev. Biochem. Vol. 81 , pp. 203-29	article	ubiquitin
Abstract: The posttranslational modification with ubiquitin, a process referred to as ubiquitylation, controls almost every process in cells. Ubiquitin can be attached to substrate proteins as a single moiety or in the form of polymeric chains in which successive ubiquitin molecules are connected through specific isopeptide bonds. Reminiscent of a code, the various ubiquitin modifications adopt distinct conformations and lead to different outcomes in cells. Here, we discuss the structure, assembly, and function of this ubiquitin code.
BibTeX: @article{KomRap12, author = {Komander, David and Rape, Michael}, title = {The ubiquitin code}, journal = {Annu. Rev. Biochem.}, year = {2012}, volume = {81}, pages = {203--29}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22524316}, doi = {http://dx.doi.org/10.1146/annurev-biochem-060310-170328} }
KucPhi08	Kuchel, P.W. & Philp, D.J.	Isotopomer subspaces as indicators of metabolic-pathway structure [Abstract] [BibTeX] [URL] [PDF]	2008	J. Theor. Biol. Vol. 252 (3) , pp. 391-401	article	metabolic, signalling
Abstract: The relative abundances and rates of formation of particular isotopic isomers (isotopomers) of metabolic intermediates from (13)C-labelled substrates in living cells provide information on the routes taken by the initial (13)C-atoms. When a primary substrate such as [U,(13)C] d-glucose is added to human erythrocytes, the pattern of labels in terminal metabolites is determined by a set of carbon-group exchange reactions in both glycolysis and the pentose phosphate pathway (PPP). Of a given terminal metabolite, not all possible isotopomers will be produced from each possible primary substrate isotopomer. There are only 8 different (13)C-isotopomers of lactate but not all of these are produced when one of the 64 possible (13)C-isotopomers of glucose is used as the input substrate; thus a subset of all 63 glucose isotopomers x 8 lactate isotopomers+1 unlabelled glucose x 1 unlabelled lactate=505 pattern associations, would be produced if a complete experimental analysis were performed with all the glucose variants. The pattern of labelling in this isotopomer subspace reflects the nature of the re-ordering reactions that 'direct' the metabolism. Predicting the combinatorial rearrangements for particular sets of reactions and comparing these with real data should enable conclusions to be drawn about which enzymes are involved in the real metabolic system. An example of the glycolysis-PPP system is discussed in the context of a debate that occurred around the F- and L-type PPPs and which one actually operates in the human RBC. As part of this discussion we introduce the term 'combinatorial deficit' of all possible isotopomers and we show that this deficit is less for the F- than the L-type pathway.
BibTeX: @article{KucPhi08, author = {Kuchel, Philip W and Philp, David J}, title = {Isotopomer subspaces as indicators of metabolic-pathway structure}, journal = {J. Theor. Biol.}, year = {2008}, volume = {252}, number = {3}, pages = {391--401}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17692871}, doi = {http://dx.doi.org/10.1016/j.jtbi.2007.05.039} }
LenSpeOch61	Lengyel, P.; Speyer, J.F. & Ochoa, S.	Synthetic polynucleotides and the amino acid code [BibTeX] [PDF]	1961	Proc. Natl. Acad. Sci. U.S.A. Vol. 47 (12) , pp. 1936-1942	article	genetic
BibTeX: @article{LenSpeOch61, author = {Lengyel, Peter and Speyer, Joseph F and Ochoa, Severo}, title = {Synthetic polynucleotides and the amino acid code}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {1961}, volume = {47}, number = {12}, pages = {1936--1942} }
MadFriRot08	Madi, A.; Friedman, Y.; Roth, D.; Regev, T.; Bransburg-Zabary, S. & Ben Jacob, E.	Genome holography: deciphering function-form motifs from gene expression data [Abstract] [BibTeX] [URL] [PDF]	2008	PloS One Vol. 3 (7) , pp. e2708	article	genetic
Abstract: DNA chips allow simultaneous measurements of genome-wide response of thousands of genes, i.e. system level monitoring of the gene-network activity. Advanced analysis methods have been developed to extract meaningful information from the vast amount of raw gene-expression data obtained from the microarray measurements. These methods usually aimed to distinguish between groups of subjects (e.g., cancer patients vs. healthy subjects) or identifying marker genes that help to distinguish between those groups. We assumed that motifs related to the internal structure of operons and gene-networks regulation are also embedded in microarray and can be deciphered by using proper analysis.
BibTeX: @article{MadFriRot08, author = {Madi, Asaf and Friedman, Yonatan and Roth, Dalit and Regev, Tamar and Bransburg-Zabary, Sharron and Ben Jacob, Eshel}, title = {Genome holography: deciphering function-form motifs from gene expression data}, journal = {PloS One}, year = {2008}, volume = {3}, number = {7}, pages = {e2708}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2444029&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1371/journal.pone.0002708} }
Mar03	Marn, O.	Thalamocortical topography reloaded: it's not where you go, but how you get there [BibTeX] [URL] [PDF]	2003	Neuron Vol. 39 (3) , pp. 388-91	article	embryology, developmental
BibTeX: @article{Mar03, author = {Marn, Oscar}, title = {Thalamocortical topography reloaded: it's not where you go, but how you get there}, journal = {Neuron}, year = {2003}, volume = {39}, number = {3}, pages = {388--91}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12895413} }
MarPfa01	Marquardt, T. & Pfaff, S.L.	Cracking the transcriptional code for cell specification in the neural tube [Abstract] [BibTeX] [URL] [PDF]	2001	Cell Vol. 106 (6) , pp. 651-4	article	brain transcription
Abstract: The bHLH repressor Olig2 participates in the transcriptional code governing cell fate specification in the ventral spinal cord. By temporally selective interactions with other transcription factors, Olig2 first directs motor neuron fate and later switches to promoting oligodendrocyte production.
BibTeX: @article{MarPfa01, author = {Marquardt, T and Pfaff, S L}, title = {Cracking the transcriptional code for cell specification in the neural tube}, journal = {Cell}, year = {2001}, volume = {106}, number = {6}, pages = {651--4}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11572771} }
MauEde07	Mauro, V.P. & Edelman, G.M.	The ribosome filter redux [BibTeX] [PDF]	2007	Cell Cycle Vol. 6 (18) , pp. 2246-2251	article	rna
BibTeX: @article{MauEde07, author = {Mauro, Vincent P and Edelman, Gerald M}, title = {The ribosome filter redux}, journal = {Cell Cycle}, year = {2007}, volume = {6}, number = {18}, pages = {2246--2251} }
MayBar09	Mayr, C. & Bartel, D.P.	Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells [Abstract] [BibTeX] [URL] [PDF]	2009	Cell Vol. 138 (4) , pp. 673-84	article	genetic
Abstract: In cancer cells, genetic alterations can activate proto-oncogenes, thereby contributing to tumorigenesis. However, the protein products of oncogenes are sometimes overexpressed without alteration of the proto-oncogene. Helping to explain this phenomenon, we found that when compared to similarly proliferating nontransformed cell lines, cancer cell lines often expressed substantial amounts of mRNA isoforms with shorter 3' untranslated regions (UTRs). These shorter isoforms usually resulted from alternative cleavage and polyadenylation (APA). The APA had functional consequences, with the shorter mRNA isoforms exhibiting increased stability and typically producing ten-fold more protein, in part through the loss of microRNA-mediated repression. Moreover, expression of the shorter mRNA isoform of the proto-oncogene IGF2BP1/IMP-1 led to far more oncogenic transformation than did expression of the full-length, annotated mRNA. The high incidence of APA in cancer cells, with consequent loss of 3'UTR repressive elements, suggests a pervasive role for APA in oncogene activation without genetic alteration.
BibTeX: @article{MayBar09, author = {Mayr, Christine and Bartel, David P}, title = {Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells}, journal = {Cell}, publisher = {Elsevier Ltd}, year = {2009}, volume = {138}, number = {4}, pages = {673--84}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2819821&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1016/j.cell.2009.06.016} }
McSGru08	McStay, B. & Grummt, I.	The epigenetics of rRNA genes: from molecular to chromosome biology [Abstract] [BibTeX] [URL] [PDF]	2008	Annu. Rev. Cell Dev. Biol. Vol. 24 , pp. 131-57	article	epigenetic
Abstract: In eukaryotes, the genes encoding ribosomal RNAs (rDNA) exist in two distinct epigenetic states that can be distinguished by a specific chromatin structure that is maintained throughout the cell cycle and is inherited from one cell to another. The fact that even in proliferating cells with a high demand of protein synthesis a fraction of rDNA is silenced provides a unique possibility to decipher the mechanism underlying epigenetic regulation of rDNA. This chapter summarizes our knowledge of the molecular mechanisms that establish and propagate the epigenetic state of rRNA genes, unraveling a complex interplay of DNA methyltransferases and histone-modifying enzymes that act in concert with chromatin remodeling complexes and RNA-guided mechanisms to define the transcriptional state of rDNA. We also review the critical role of the RNA polymerase I transcription factor UBF in the formation of active nucleolar organizer regions (NORs) and maintenance of the euchromatic state of rRNA genes.
BibTeX: @article{McSGru08, author = {McStay, Brian and Grummt, Ingrid}, title = {The epigenetics of rRNA genes: from molecular to chromosome biology}, journal = {Annu. Rev. Cell Dev. Biol.}, year = {2008}, volume = {24}, pages = {131--57}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18616426}, doi = {http://dx.doi.org/10.1146/annurev.cellbio.24.110707.175259} }
MeiHar02	Meiklejohn, C.D. & Hartl, D.L.	A single mode of canalization [BibTeX] [URL] [PDF]	2002	Trends Ecol. Evol. Vol. 17 (10) , pp. 468-473	article	embryology, developmental
BibTeX: @article{MeiHar02, author = {Meiklejohn, Colin D. and Hartl, Daniel L.}, title = {A single mode of canalization}, journal = {Trends Ecol. Evol.}, year = {2002}, volume = {17}, number = {10}, pages = {468--473}, url = {http://linkinghub.elsevier.com/retrieve/pii/S016953470202596X}, doi = {http://dx.doi.org/10.1016/S0169-5347(02)02596-X} }
MicYod06	Michaud, E.J. & Yoder, B.K.	The primary cilium in cell signaling and cancer [Abstract] [BibTeX] [URL] [PDF]	2006	Cancer Res. Vol. 66 (13) , pp. 6463-7	article	embryology, developmental
Abstract: The primary cilium is a microtubule-based antenna-like structure that emanates from the surface of virtually all cells in the mammalian body. It is anchored to the cell by the basal body, which develops from the mother centriole of the centrosome in a manner that is coordinately regulated with the cell cycle. The primary cilium is a sensory organelle that receives both mechanical and chemical signals from other cells and the environment, and transmits these signals to the nucleus to elicit a cellular response. Recent studies revealed that multiple components of the Sonic hedgehog and platelet-derived growth factor receptor-alpha signal transduction pathways localize to the primary cilium, and that loss of the cilium blocks ligand-induced signaling by both pathways. In light of the major role that these pathways play in numerous types of cancer, we anticipate that the emerging discoveries being made about the function of the primary cilium in signaling pathways that are critical for embryonic development and tissue homeostasis in adults will also provide novel insights into the molecular mechanisms of carcinogenesis.
BibTeX: @article{MicYod06, author = {Michaud, Edward J and Yoder, Bradley K}, title = {The primary cilium in cell signaling and cancer}, journal = {Cancer Res.}, year = {2006}, volume = {66}, number = {13}, pages = {6463--7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16818613}, doi = {http://dx.doi.org/10.1158/0008-5472.CAN-06-0462} }
MikFri05	Mikkers, H. & Frisén, J.	Deconstructing stemness [Abstract] [BibTeX] [URL] [PDF]	2005	EMBO J. Vol. 24 (15) , pp. 2715-9	article	embryology, developmental
Abstract: Stem cells are unique in their capacity to self-renew and generate differentiated progeny to maintain tissues throughout life. A common molecular program for stem cells has remained elusive. We discuss what the molecular logic of stemness may be. We suggest that it may not be coupled to distinct cellular properties such as self-renewal or multipotency, but rather to the stable suspension at a specific developmental stage. In this view, the stem cell niche allows a cell to maintain a transcriptional accessibility enabling the generation of specific differentiated progeny.
BibTeX: @article{MikFri05, author = {Mikkers, Harald and Frisén, Jonas}, title = {Deconstructing stemness}, journal = {EMBO J.}, year = {2005}, volume = {24}, number = {15}, pages = {2715--9}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1182244&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1038/sj.emboj.7600749} }
MitGro08	Mitrophanov, A.Y. & Groisman, E.	Positive feedback in cellular control systems [Abstract] [BibTeX] [URL] [PDF]	2008	BioEssays Vol. 30 (6) , pp. 542-55	article	metabolic, signalling
Abstract: Feedback loops have been identified in a variety of regulatory systems and organisms. While feedback loops of the same type (negative or positive) tend to have properties in common, they can play distinctively diverse roles in different regulatory systems, where they can affect virulence in a pathogenic bacterium, maturation patterns of vertebrate oocytes and transitions through cell cycle phases in eukaryotic cells. This review focuses on the properties and functions of positive feedback in biological systems, including bistability, hysteresis and activation surges.
BibTeX: @article{MitGro08, author = {Mitrophanov, Alexander Y and Groisman, Eduardo}, title = {Positive feedback in cellular control systems}, journal = {BioEssays}, year = {2008}, volume = {30}, number = {6}, pages = {542--55}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2486260&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1002/bies.20769} }
MooSau07	Moore, S.D. & Sauer, R.T.	The tmRNA system for translational surveillance and ribosome rescue [Abstract] [BibTeX] [URL] [PDF]	2007	Annu. Rev. Biochem. Vol. 76 , pp. 101-24	article	rna
Abstract: The tmRNA system performs translational surveillance and ribosome rescue in all eubacteria and some eukaryotic organelles. This system intervenes when ribosomes read to the 3' end of an mRNA or pause at internal codons with subsequent mRNA cleavage. A complex of alanyl-tmRNA (which functions as a tRNA and mRNA), SmpB protein, and EF-TucGTP binds stalled ribosomes, the nascent polypeptide is transferred to the alanine on tmRNA, and translation switches from the original message to a short tmRNA open reading frame (ORF) that encodes a degradation tag. Translation of the ORF and normal termination releases the tagged polypeptide for degradation and permits disassembly and recycling of ribosomal subunits for new rounds of protein synthesis. Structural and biochemical studies suggest mechanisms that keep tmRNA from interrupting normal translation and target ribosomes stalled with very short 3' mRNA extensions. Additional biological roles of tmRNA include stress management and the regulation of transcriptional circuits.
BibTeX: @article{MooSau07, author = {Moore, Sean D. and Sauer, Robert T.}, title = {The tmRNA system for translational surveillance and ribosome rescue}, journal = {Annu. Rev. Biochem.}, year = {2007}, volume = {76}, pages = {101--24}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17291191}, doi = {http://dx.doi.org/10.1146/annurev.biochem.75.103004.142733} }
Mur06	Murphy, R.F.	Putting proteins on the map [BibTeX] [PDF]	2006	Nat. Biotechnol. Vol. 24 (10) , pp. 1223-1224	article	compartment
BibTeX: @article{Mur06, author = {Murphy, Robert F}, title = {Putting proteins on the map}, journal = {Nat. Biotechnol.}, year = {2006}, volume = {24}, number = {10}, pages = {1223--1224} }
Mur02	Murren, C.J.	Phenotypic integration in plants [BibTeX] [URL] [PDF]	2002	Plant Spec. Biol. Vol. 17 (2-3) , pp. 89-99	article	embryology, developmental
BibTeX: @article{Mur02, author = {Murren, Courtney J.}, title = {Phenotypic integration in plants}, journal = {Plant Spec. Biol.}, year = {2002}, volume = {17}, number = {2-3}, pages = {89--99}, url = {http://doi.wiley.com/10.1046/j.1442-1984.2002.00079.x}, doi = {http://dx.doi.org/10.1046/j.1442-1984.2002.00079.x} }
Mus93	Muslimov, I. a.	The ribosome as a source of genome hypervariability? [Abstract] [BibTeX] [URL] [PDF]	1993	Med. Hypotheses Vol. 41 (3) , pp. 201-4	article	rna
Abstract: In this report it is suggested that at early stages of evolution ribosomes were responsible for synthesizing short oligonucleotide cDNA packets which formed the protogenic tandem repetitive sequences. Ribosomal RNA (rRNA) could have been the most probable template for such a synthesis. rRNA has homology with the monomers of tandem hypervariable repetitive elements of the genome. A model for the proposed participation of rRNA in the genesis of genomic fragments is provided by analysis of the active center of GTP-binding proteins. The role of oligonucleotides, synthesized by the ribosome, in the context of mechanisms of genome regulation, genes responsible for disease and human longterm memory formation are also discussed.
BibTeX: @article{Mus93, author = {Muslimov, I a}, title = {The ribosome as a source of genome hypervariability?}, journal = {Med. Hypotheses}, year = {1993}, volume = {41}, number = {3}, pages = {201--4}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8259075} }
Nei07	Nei, M.	The new mutation theory of phenotypic evolution [Abstract] [BibTeX] [URL] [PDF]	2007	Proc. Natl. Acad. Sci. U.S.A. Vol. 104 (30) , pp. 12235-42	article	genetic
Abstract: Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.
BibTeX: @article{Nei07, author = {Nei, Masatoshi}, title = {The new mutation theory of phenotypic evolution}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2007}, volume = {104}, number = {30}, pages = {12235--42}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1941456&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1073/pnas.0703349104} }
NicRib06	Nicolelis, M.A.L. & Ribeiro, S.	Seeking the neural code [BibTeX] [PDF]	2006	Sci. Amer. (December) , pp. 70-77	article	neural
BibTeX: @article{NicRib06, author = {Nicolelis, Miguel A L and Ribeiro, Sidarta}, title = {Seeking the neural code}, journal = {Sci. Amer.}, year = {2006}, number = {December}, pages = {70--77} }
NirLed64	Nirenberg, M. & Leder, P.	RNA codewords and protein synthesis [BibTeX] [PDF]	1964	Science Vol. 145 (3639) , pp. 1399-1407	article	genetic
BibTeX: @article{NirLed64, author = {Nirenberg, Marshall and Leder, Phillip}, title = {RNA codewords and protein synthesis}, journal = {Science}, year = {1964}, volume = {145}, number = {3639}, pages = {1399--1407} }
NirMat61	Nirenberg, M.W. & Matthaei, J.H.	The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides [BibTeX] [PDF]	1961	Proc. Natl. Acad. Sci. U.S.A. Vol. 47 (10) , pp. 1588-1602	article	genetic
BibTeX: @article{NirMat61, author = {Nirenberg, Marshall W and Matthaei, J. Heinrich}, title = {The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {1961}, volume = {47}, number = {10}, pages = {1588--1602} }
OsbPalLis08	Osborne, L.C.; Palmer, S.E.; Lisberger, S.G. & Bialek, W.	The neural basis for combinatorial coding in a cortical population response [Abstract] [BibTeX] [URL] [PDF]	2008	J. Neurosci. Vol. 28 (50) , pp. 13522-31	article	neural
Abstract: We have used a combination of theory and experiment to assess how information is represented in a realistic cortical population response, examining how motion direction and timing is encoded in groups of neurons in cortical area MT. Combining data from several single-unit experiments, we constructed model population responses in small time windows and represented the response in each window as a binary vector of 1s or 0s signifying spikes or no spikes from each cell. We found that patterns of spikes and silence across a population of nominally redundant neurons can carry up to twice as much information about visual motion than does population spike count, even when the neurons respond independently to their sensory inputs. This extra information arises by virtue of the broad diversity of firing rate dynamics found in even very similarly tuned groups of MT neurons. Additionally, specific patterns of spiking and silence can carry more information than the sum of their parts (synergy), opening up the possibility for combinatorial coding in cortex. These results also held for populations in which we imposed levels of nonindependence (correlation) comparable to those found in cortical recordings. Our findings suggest that combinatorial codes are advantageous for representing stimulus information on short time scales, even when neurons have no complicated, stimulus-dependent correlation structure.
BibTeX: @article{OsbPalLis08, author = {Osborne, Leslie C and Palmer, Stephanie E and Lisberger, Stephen G and Bialek, William}, title = {The neural basis for combinatorial coding in a cortical population response}, journal = {J. Neurosci.}, year = {2008}, volume = {28}, number = {50}, pages = {13522--31}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2693376&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1523/JNEUROSCI.4390-08.2008} }
PapZwaJan09	Papoutsi, M.; de Zwart, J. a.; Jansma, J.M.; Pickering, M.J.; Bednar, J. a. & Horwitz, B.	From phonemes to articulatory codes: an fMRI study of the role of Broca's area in speech production [Abstract] [BibTeX] [URL] [PDF]	2009	Cereb. Cortex Vol. 19 (9) , pp. 2156-65	article	brain transcription
Abstract: We used event-related functional magnetic resonance imaging to investigate the neuroanatomical substrates of phonetic encoding and the generation of articulatory codes from phonological representations. Our focus was on the role of the left inferior frontal gyrus (LIFG) and in particular whether the LIFG plays a role in sublexical phonological processing such as syllabification or whether it is directly involved in phonetic encoding and the generation of articulatory codes. To answer this question, we contrasted the brain activation patterns elicited by pseudowords with high- or low-sublexical frequency components, which we expected would reveal areas related to the generation of articulatory codes but not areas related to phonological encoding. We found significant activation of a premotor network consisting of the dorsal precentral gyrus, the inferior frontal gyrus bilaterally, and the supplementary motor area for low- versus high-sublexical frequency pseudowords. Based on our hypothesis, we concluded that these areas and in particular the LIFG are involved in phonetic and not phonological encoding. We further discuss our findings with respect to the mechanisms of phonetic encoding and provide evidence in support of a functional segregation of the posterior part of Broca's area, the pars opercularis.
BibTeX: @article{PapZwaJan09, author = {Papoutsi, Marina and de Zwart, Jacco a and Jansma, J Martijn and Pickering, Martin J and Bednar, James a and Horwitz, Barry}, title = {From phonemes to articulatory codes: an fMRI study of the role of Broca's area in speech production}, journal = {Cereb. Cortex}, year = {2009}, volume = {19}, number = {9}, pages = {2156--65}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2722428&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1093/cercor/bhn239} }
PeaCulWin07	Pearson, C.G.; Culver, B.P. & Winey, M.	Centrioles want to move out and make cilia [Abstract] [BibTeX] [URL] [PDF]	2007	Dev. Cell Vol. 13 (3) , pp. 319-21	article	embryology, developmental
Abstract: Cilia formation in mammalian cells requires basal bodies that are either derived from centrioles that transition from their cytoplasmic role in centrosome organization or that form en masse in multiciliated cells. Several recent studies have begun to uncover the links between centriole duplication and their transformation to basal bodies.
BibTeX: @article{PeaCulWin07, author = {Pearson, Chad G and Culver, Brady P and Winey, Mark}, title = {Centrioles want to move out and make cilia}, journal = {Dev. Cell}, year = {2007}, volume = {13}, number = {3}, pages = {319--21}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17765674}, doi = {http://dx.doi.org/10.1016/j.devcel.2007.08.007} }
PerRos05	Perissi, V. & Rosenfeld, M.G.	Controlling nuclear receptors: the circular logic of cofactor cycles [BibTeX] [URL] [PDF]	2005	Nat. Rev. Mol. Cell Biol. Vol. 6 (7) , pp. 542-554	article	acetylation
BibTeX: @article{PerRos05, author = {Perissi, Valentina and Rosenfeld, Michael G.}, title = {Controlling nuclear receptors: the circular logic of cofactor cycles}, journal = {Nat. Rev. Mol. Cell Biol.}, year = {2005}, volume = {6}, number = {7}, pages = {542--554}, url = {http://www.nature.com/doifinder/10.1038/nrm1680}, doi = {http://dx.doi.org/10.1038/nrm1680} }
PerMouSal07	Pertea, M.; Mount, S.M. & Salzberg, S.L.	A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana [Abstract] [BibTeX] [URL] [PDF]	2007	BMC Bioinformatics Vol. 8 , pp. 159	article	splicing
Abstract: Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites.
BibTeX: @article{PerMouSal07, author = {Pertea, Mihaela and Mount, Stephen M and Salzberg, Steven L}, title = {A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana}, journal = {BMC Bioinformatics}, year = {2007}, volume = {8}, pages = {159}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1892810&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1186/1471-2105-8-159} }
Pta08	Ptashne, M.	Transcription: a mechanism for short-term memory [Abstract] [BibTeX] [URL] [PDF]	2008	Curr. Biol. Vol. 18 (1) , pp. R25-7	article	epigenetic
Abstract: Yeast growing for a considerable time in glucose 'remember' a previous exposure to galactose, the inducer of its galactose-utilization (GAL) genes. This memory is conveyed by a cytoplasmically transmitted galactokinase working as a signal transducer.
BibTeX: @article{Pta08, author = {Ptashne, Mark}, title = {Transcription: a mechanism for short-term memory}, journal = {Curr. Biol.}, year = {2008}, volume = {18}, number = {1}, pages = {R25--7}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18177708}, doi = {http://dx.doi.org/10.1016/j.cub.2007.11.017} }
RanVer07	Rando, O.J. & Verstrepen, K.J.	Timescales of genetic and epigenetic inheritance [Abstract] [BibTeX] [URL] [PDF]	2007	Cell Vol. 128 (4) , pp. 655-68	article	epigenetic
Abstract: According to classical evolutionary theory, phenotypic variation originates from random mutations that are independent of selective pressure. However, recent findings suggest that organisms have evolved mechanisms to influence the timing or genomic location of heritable variability. Hypervariable contingency loci and epigenetic switches increase the variability of specific phenotypes; error-prone DNA replicases produce bursts of variability in times of stress. Interestingly, these mechanisms seem to tune the variability of a given phenotype to match the variability of the acting selective pressure. Although these observations do not undermine Darwin's theory, they suggest that selection and variability are less independent than once thought.
BibTeX: @article{RanVer07, author = {Rando, Oliver J and Verstrepen, Kevin J}, title = {Timescales of genetic and epigenetic inheritance}, journal = {Cell}, year = {2007}, volume = {128}, number = {4}, pages = {655--68}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17320504}, doi = {http://dx.doi.org/10.1016/j.cell.2007.01.023} }
RavSomMon02	Ravasz, E.; Somera, a.L.; Mongru, D. a.; Oltvai, Z.N. & Barabási, a.L.	Hierarchical organization of modularity in metabolic networks [Abstract] [BibTeX] [URL] [PDF]	2002	Science Vol. 297 (5586) , pp. 1551-5	article	metabolic, signalling
Abstract: Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated biochemical networks lacks quantitative support. Here, we show that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law. Within Escherichia coli, the uncovered hierarchical modularity closely overlaps with known metabolic functions. The identified network architecture may be generic to system-level cellular organization.
BibTeX: @article{RavSomMon02, author = {Ravasz, E and Somera, a L and Mongru, D a and Oltvai, Z N and Barabási, a L}, title = {Hierarchical organization of modularity in metabolic networks}, journal = {Science}, year = {2002}, volume = {297}, number = {5586}, pages = {1551--5}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12202830}, doi = {http://dx.doi.org/10.1126/science.1073374} }
RayNatShi07	Ray, A.; van Naters, W.V.D.G.; Shiraiwa, T. & Carlson, J.R.	Mechanisms of odor receptor gene choice in Drosophila [Abstract] [BibTeX] [URL] [PDF]	2007	Neuron Vol. 53 (3) , pp. 353-69	article	brain transcription
Abstract: A remarkable problem in neurobiology is how olfactory receptor neurons (ORNs) select, from among a large odor receptor repertoire, which receptors to express. We use computational algorithms and mutational analysis to define positive and negative regulatory elements that are required for selection of odor receptor (Or) genes in the proper olfactory organ of Drosophila, and we identify an element that is essential for selection in one ORN class. Two odor receptors are coexpressed by virtue of the alternative splicing of a single gene, and we identify dicistronic mRNAs that each encode two receptors. Systematic analysis reveals no evidence for negative feedback regulation, but provides evidence that the choices made by neighboring ORNs of a sensillum are coordinated via the asymmetric segregation of regulatory factors from a common progenitor. We show that receptor gene choice in Drosophila also depends on a combinatorial code of transcription factors to generate the receptor-to-neuron map.
BibTeX: @article{RayNatShi07, author = {Ray, Anandasankar and van Naters, Wynand Van Der Goes and Shiraiwa, Takashi and Carlson, John R}, title = {Mechanisms of odor receptor gene choice in Drosophila}, journal = {Neuron}, year = {2007}, volume = {53}, number = {3}, pages = {353--69}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1986798&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1016/j.neuron.2006.12.010} }
Rei07	Reik, W.	Stability and flexibility of epigenetic gene regulation in mammalian development [Abstract] [BibTeX] [URL] [PDF]	2007	Nature Vol. 447 (7143) , pp. 425-32	article	epigenetic
Abstract: During development, cells start in a pluripotent state, from which they can differentiate into many cell types, and progressively develop a narrower potential. Their gene-expression programmes become more defined, restricted and, potentially, 'locked in'. Pluripotent stem cells express genes that encode a set of core transcription factors, while genes that are required later in development are repressed by histone marks, which confer short-term, and therefore flexible, epigenetic silencing. By contrast, the methylation of DNA confers long-term epigenetic silencing of particular sequences--transposons, imprinted genes and pluripotency-associated genes--in somatic cells. Long-term silencing can be reprogrammed by demethylation of DNA, and this process might involve DNA repair. It is not known whether any of the epigenetic marks has a primary role in determining cell and lineage commitment during development.
BibTeX: @article{Rei07, author = {Reik, Wolf}, title = {Stability and flexibility of epigenetic gene regulation in mammalian development}, journal = {Nature}, year = {2007}, volume = {447}, number = {7143}, pages = {425--32}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17522676}, doi = {http://dx.doi.org/10.1038/nature05918} }
RodEgg06	Rodolfa, K.T. & Eggan, K.	A transcriptional logic for nuclear reprogramming [Abstract] [BibTeX] [URL] [PDF]	2006	Cell Vol. 126 (4) , pp. 652-5	article	nucleosome
Abstract: Limitations on a differentiated cell's pluripotency can be erased by nuclear transfer or by fusion with embryonic stem cells, but attempts to recapitulate this process of nuclear reprogramming by molecular means have failed. In this issue of Cell, Takahashi and Yamanaka (2006) take a rational approach to identifying a suite of embryonic transcription factors whose overexpression restores pluripotency to adult somatic cells.
BibTeX: @article{RodEgg06, author = {Rodolfa, Kit T and Eggan, Kevin}, title = {A transcriptional logic for nuclear reprogramming}, journal = {Cell}, year = {2006}, volume = {126}, number = {4}, pages = {652--5}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16923385}, doi = {http://dx.doi.org/10.1016/j.cell.2006.08.009} }
RoeParHaa09	Roelofs, J.; Park, S.; Haas, W.; Tian, G.; McAllister, F.E.; Huo, Y.; Lee, B.-H.; Zhang, F.; Shi, Y.; Gygi, S.P. & Finley, D.	Chaperone-mediated pathway of proteasome regulatory particle assembly [Abstract] [BibTeX] [URL] [PDF]	2009	Nature Vol. 459 (7248) , pp. 861-5	article	folding
Abstract: The proteasome is a protease that controls diverse processes in eukaryotic cells. Its regulatory particle (RP) initiates the degradation of ubiquitin-protein conjugates by unfolding the substrate and translocating it into the proteasome core particle (CP) to be degraded. The RP has 19 subunits, and their pathway of assembly is not understood. Here we show that in the yeast Saccharomyces cerevisiae three proteins are found associated with RP but not with the RP-CP holoenzyme: Nas6, Rpn14 and Hsm3. Mutations in the corresponding genes confer proteasome loss-of-function phenotypes, despite their virtual absence from the holoenzyme. These effects result from deficient RP assembly. Thus, Nas6, Rpn14 and Hsm3 are RP chaperones. The RP contains six ATPases-the Rpt proteins-and each RP chaperone binds to the carboxy-terminal domain of a specific Rpt. We show in an accompanying study that RP assembly is templated through the Rpt C termini, apparently by their insertion into binding pockets in the CP. Thus, RP chaperones may regulate proteasome assembly by directly restricting the accessibility of Rpt C termini to the CP. In addition, competition between the RP chaperones and the CP for Rpt engagement may explain the release of RP chaperones as proteasomes mature.
BibTeX: @article{RoeParHaa09, author = {Roelofs, Jeroen and Park, Soyeon and Haas, Wilhelm and Tian, Geng and McAllister, Fiona E and Huo, Ying and Lee, Byung-Hoon and Zhang, Fan and Shi, Yigong and Gygi, Steven P and Finley, Daniel}, title = {Chaperone-mediated pathway of proteasome regulatory particle assembly}, journal = {Nature}, publisher = {Nature Publishing Group}, year = {2009}, volume = {459}, number = {7248}, pages = {861--5}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2727592&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1038/nature08063} }
RokShlSha07	Rokhlenko, O.; Shlomi, T.; Sharan, R.; Ruppin, E. & Pinter, R.Y.	Constraint-based functional similarity of metabolic genes: going beyond network topology [Abstract] [BibTeX] [URL] [PDF]	2007	Bioinformatics Vol. 23 (16) , pp. 2139-46	article	metabolic, signalling
Abstract: Several recent studies attempted to establish measures for the similarity between genes that are based on the topological properties of metabolic networks. However, these approaches offer only a static description of the properties of interest and offer moderate (albeit significant) correlations with pertinent experimental data.
BibTeX: @article{RokShlSha07, author = {Rokhlenko, Oleg and Shlomi, Tomer and Sharan, Roded and Ruppin, Eytan and Pinter, Ron Y}, title = {Constraint-based functional similarity of metabolic genes: going beyond network topology}, journal = {Bioinformatics}, year = {2007}, volume = {23}, number = {16}, pages = {2139--46}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17586548}, doi = {http://dx.doi.org/10.1093/bioinformatics/btm319} }
RuiMasSte07	Ruiz i Altaba, A.; Mas, C. & Stecca, B.	The Gli code: an information nexus regulating cell fate, stemness and cancer [Abstract] [BibTeX] [URL] [PDF]	2007	Trends Cell Biol. Vol. 17 (9) , pp. 438-47	article	brain transcription
Abstract: The Gli code hypothesis postulates that the three vertebrate Gli transcription factors act together in responding cells to integrate intercellular Hedgehog (Hh) and other signaling inputs, resulting in the regulation of tissue pattern, size and shape. Hh and other inputs are then just ways to modify the Gli code. Recent data confirm this idea and suggest that the Gli code regulates stemness and also tumor progression and metastatic growth, opening exciting possibilities for both regenerative medicine and novel anticancer therapies.
BibTeX: @article{RuiMasSte07, author = {Ruiz i Altaba, Ariel and Mas, Christophe and Stecca, Barbara}, title = {The Gli code: an information nexus regulating cell fate, stemness and cancer}, journal = {Trends Cell Biol.}, year = {2007}, volume = {17}, number = {9}, pages = {438--47}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2601665&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1016/j.tcb.2007.06.007} }
RuiNguPal03	Ruiz i Altaba, A.; Nguyên, V. & Palma, V.	The emergent design of the neural tube: prepattern, SHH morphogen and Gli code [BibTeX] [URL] [PDF]	2003	Curr. Opin. Genet. Dev. Vol. 13 (5) , pp. 513-521	article	neural
BibTeX: @article{RuiNguPal03, author = {Ruiz i Altaba, Ariel and Nguyên, Vân and Palma, Verónica}, title = {The emergent design of the neural tube: prepattern, SHH morphogen and Gli code}, journal = {Curr. Opin. Genet. Dev.}, year = {2003}, volume = {13}, number = {5}, pages = {513--521}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0959437X03001163}, doi = {http://dx.doi.org/10.1016/j.gde.2003.08.005} }
RumHoaMay01	Rumbley, J.; Hoang, L.; Mayne, L. & Englander, S.W.	An amino acid code for protein folding [BibTeX] [PDF]	2001	Proc. Natl. Acad. Sci. U.S.A. Vol. 98 (1) , pp. 105-112	article	folding
BibTeX: @article{RumHoaMay01, author = {Rumbley, Jon and Hoang, Linh and Mayne, Leland and Englander, S Walter}, title = {An amino acid code for protein folding}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2001}, volume = {98}, number = {1}, pages = {105--112} }
SakSamAbe94	Saks, M.E.; Sampson, J.R. & Abelson, J.N.	RNA the transfer a search problem : identity for rules [BibTeX] [PDF]	1994	Science Vol. 263 (5144) , pp. 191-197	article	genetic
BibTeX: @article{SakSamAbe94, author = {Saks, Margaret E and Sampson, Jeffrey R and Abelson, John N}, title = {RNA the transfer a search problem : identity for rules}, journal = {Science}, year = {1994}, volume = {263}, number = {5144}, pages = {191--197} }
SatChr07	Satir, P. & Christensen, S. r.T.	Overview of structure and function of mammalian cilia [Abstract] [BibTeX] [URL] [PDF]	2007	Annu. Rev. Physiol. Vol. 69 , pp. 377-400	article	embryology, developmental
Abstract: Cilia are membrane-bounded, centriole-derived projections from the cell surface that contain a microtubule cytoskeleton, the ciliary axoneme, surrounded by a ciliary membrane. Axonemes in multiciliated cells of mammalian epithelia are 9 + 2, possess dynein arms, and are motile. In contrast, single nonmotile 9 + 0 primary cilia are found on epithelial cells, such as those of the kidney tubule, but also on nonepithelial cells, such as chondrocytes, fibroblasts, and neurons. The ciliary membranes of all cilia contain specific receptors and ion channel proteins that initiate signaling pathways controlling motility and/or linking mechanical or chemical stimuli, including sonic hedgehog and growth factors, to intracellular transduction cascades regulating differentiation, migration, and cell growth during development and in adulthood. Unique motile 9 + 0 cilia, found during development at the embryonic node, determine left-right asymmetry of the body.
BibTeX: @article{SatChr07, author = {Satir, Peter and Christensen, Sø ren Tvorup}, title = {Overview of structure and function of mammalian cilia}, journal = {Annu. Rev. Physiol.}, year = {2007}, volume = {69}, pages = {377--400}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17009929}, doi = {http://dx.doi.org/10.1146/annurev.physiol.69.040705.141236} }
Sch07	Schubert, W.	A three-symbol code for organized proteomes based on cyclical imaging of protein locations [BibTeX] [PDF]	2007	Cytom. Part A Vol. 71 (A) , pp. 352-360	article	compartment
BibTeX: @article{Sch07, author = {Schubert, Walter}, title = {A three-symbol code for organized proteomes based on cyclical imaging of protein locations}, journal = {Cytom. Part A}, year = {2007}, volume = {71}, number = {A}, pages = {352--360}, doi = {http://dx.doi.org/10.1002/cyto.a} }
SchBonPom06	Schubert, W.; Bonnekoh, B.; Pommer, A.J.; Philipsen, L.; Böckelmann, R.; Malykh, Y.; Gollnick, H.; Friedenberger, M.; Bode, M. & Dress, A.W.M.	Analyzing proteome topology and function by automated multidimensional fluorescence microscopy [Abstract] [BibTeX] [URL] [PDF]	2006	Nat. Biotechnol. Vol. 24 (10) , pp. 1270-8	article	compartment
Abstract: Temporal and spatial regulation of proteins contributes to function. We describe a multidimensional microscopic robot technology for high-throughput protein colocalization studies that runs cycles of fluorescence tagging, imaging and bleaching in situ. This technology combines three advances: a fluorescence technique capable of mapping hundreds of different proteins in one tissue section or cell sample; a method selecting the most prominent combinatorial molecular patterns by representing the data as binary vectors; and a system for imaging the distribution of these protein clusters in a so-called toponome map. By analyzing many cell and tissue types, we show that this approach reveals rules of hierarchical protein network organization, in which the frequency distribution of different protein clusters obeys Zipf's law, and state-specific lead proteins appear to control protein network topology and function. The technology may facilitate the development of diagnostics and targeted therapies.
BibTeX: @article{SchBonPom06, author = {Schubert, Walter and Bonnekoh, Bernd and Pommer, Ansgar J and Philipsen, Lars and Böckelmann, Raik and Malykh, Yanina and Gollnick, Harald and Friedenberger, Manuela and Bode, Marcus and Dress, Andreas W M}, title = {Analyzing proteome topology and function by automated multidimensional fluorescence microscopy}, journal = {Nat. Biotechnol.}, year = {2006}, volume = {24}, number = {10}, pages = {1270--8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17013374}, doi = {http://dx.doi.org/10.1038/nbt1250} }
ScuRos02	Scully, K.M. & Rosenfeld, M.G.	Pituitary development: regulatory codes in mammalian organogenesis [Abstract] [BibTeX] [URL] [PDF]	2002	Science Vol. 295 (5563) , pp. 2231-5	article	acetylation
Abstract: During mammalian pituitary gland development, distinct cell types emerge from a common primordium. Appearance of specific cell types occurs in response to opposing signaling gradients that emanate from distinct organizing centers. These signals induce expression of interacting transcriptional regulators, including DNA binding-dependent activators and DNA binding-independent transrepressors, in temporally and spatially overlapping patterns. Together they synergistically regulate precursor proliferation and induction of distinct cell types. Terminal cell type differentiation requires selective gene activation strategies and long-term active repression, mediated by cell type-specific and promoter-specific recruitment of coregulatory complexes. These mechanisms imply the potential for flexibility in the ultimate identity of differentiated cell types.
BibTeX: @article{ScuRos02, author = {Scully, Kathleen M and Rosenfeld, Michael G}, title = {Pituitary development: regulatory codes in mammalian organogenesis}, journal = {Science}, year = {2002}, volume = {295}, number = {5563}, pages = {2231--5}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11910101}, doi = {http://dx.doi.org/10.1126/science.1062736} }
SegFonChe06	Segal, E.; Fondufe-Mittendorf, Y.; Chen, L.; Thå ström, A.; Field, Y.; Moore, I.K.; Wang, J.-P.Z. & Widom, J.	A genomic code for nucleosome positioning [Abstract] [BibTeX] [URL] [PDF]	2006	Nature Vol. 442 (7104) , pp. 772-8	article	nucleosome
Abstract: Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome-DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain approximately 50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.
BibTeX: @article{SegFonChe06, author = {Segal, Eran and Fondufe-Mittendorf, Yvonne and Chen, Lingyi and Thå ström, AnnChristine and Field, Yair and Moore, Irene K and Wang, Ji-Ping Z and Widom, Jonathan}, title = {A genomic code for nucleosome positioning}, journal = {Nature}, year = {2006}, volume = {442}, number = {7104}, pages = {772--8}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2623244&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1038/nature04979} }
SenYanHig07	Sengupta, S.; Yang, X. & Higgs, P.G.	The mechanisms of codon reassignments in mitochondrial genetic codes [Abstract] [BibTeX] [URL] [PDF]	2007	J. Mol. Evol. Vol. 64 (6) , pp. 662-88	article	genetic
Abstract: Many cases of nonstandard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The "gain" represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The "loss" represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is codon disappearance (CD), where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the unassigned codon mechanism, the loss occurs first, whereas in the ambiguous intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. CD is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense-to-sense reassignments cannot be explained by CD. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the unassigned codon and the ambiguous intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.
BibTeX: @article{SenYanHig07, author = {Sengupta, Supratim and Yang, Xiaoguang and Higgs, Paul G}, title = {The mechanisms of codon reassignments in mitochondrial genetic codes}, journal = {J. Mol. Evol.}, year = {2007}, volume = {64}, number = {6}, pages = {662--88}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1894752&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1007/s00239-006-0284-7} }
ShaNud06	Shamovsky, I. & Nudler, E.	Gene control by large noncoding RNAs [Abstract] [BibTeX] [URL] [PDF]	2006	Sci. STKE Vol. 2006 (355) , pp. pe40	article	rna
Abstract: Large noncoding RNAs (lncRNAs) have emerged as key players in regulating various fundamental cellular processes. Recent reports identify a functional lncRNA, Evf-2, that operates during development to control the expression of specific homeodomain proteins, and they provide important insights into the mechanism of cooperation between a newly discovered nuclear receptor co-repressor protein (SLIRP) and steroid receptor activator RNA. Evf-2 is the first example of lncRNA directly involved in organogenesis in vertebrates.
BibTeX: @article{ShaNud06, author = {Shamovsky, Ilya and Nudler, Evgeny}, title = {Gene control by large noncoding RNAs}, journal = {Sci. STKE}, year = {2006}, volume = {2006}, number = {355}, pages = {pe40}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17018852}, doi = {http://dx.doi.org/10.1126/stke.3552006pe40} }
SheWanDim06	Shen, Q.; Wang, Y.; Dimos, J.T.; Fasano, C. a.; Phoenix, T.N.; Lemischka, I.R.; Ivanova, N.B.; Stifani, S.; Morrisey, E.E. & Temple, S.	The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells [Abstract] [BibTeX] [URL] [PDF]	2006	Nat. Neurosci. Vol. 9 (6) , pp. 743-51	article	brain transcription
Abstract: In the developing cerebral cortex, neurons are born on a predictable schedule. Here we show in mice that the essential timing mechanism is programmed within individual progenitor cells, and its expression depends solely on cell-intrinsic and environmental factors generated within the clonal lineage. Multipotent progenitor cells undergo repeated asymmetric divisions, sequentially generating neurons in their normal in vivo order: first preplate cells, including Cajal-Retzius neurons, then deep and finally superficial cortical plate neurons. As each cortical layer arises, stem cells and neuroblasts become restricted from generating earlier-born neuron types. Growth as neurospheres or in co-culture with younger cells did not restore their plasticity. Using short-hairpin RNA (shRNA) to reduce Foxg1 expression reset the timing of mid- but not late-gestation progenitors, allowing them to remake preplate neurons and then cortical-plate neurons. Our data demonstrate that neural stem cells change neuropotency during development and have a window of plasticity when restrictions can be reversed.
BibTeX: @article{SheWanDim06, author = {Shen, Qin and Wang, Yue and Dimos, John T and Fasano, Christopher a and Phoenix, Timothy N and Lemischka, Ihor R and Ivanova, Natalia B and Stifani, Stefano and Morrisey, Edward E and Temple, Sally}, title = {The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells}, journal = {Nat. Neurosci.}, year = {2006}, volume = {9}, number = {6}, pages = {743--51}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16680166}, doi = {http://dx.doi.org/10.1038/nn1694} }
SimRei08	Sims, R.J. & Reinberg, D.	Is there a code embedded in proteins that is based on post-translational modifications? [Abstract] [BibTeX] [URL] [PDF]	2008	Nat. Rev. Mol. Cell Biol. Vol. 9 (10) , pp. 815-20	article	histone
Abstract: Covalent post-translational modifications (PTMs) provide vast indexing potential and expanded protein use. The 'histone code' hypothesis has inspired rapid advances throughout chromatin biology, and has recently been tapped for its relevance to non-histone proteins. Comprehensive analyses suggest that rather than constituting a general code, the covalent modifications of proteins (including histones) provide surfaces that are recognized by effectors that can give rise to intricate interactions and downstream events. These are reminiscent of other regulatory cascades in transcription and cell signalling.
BibTeX: @article{SimRei08, author = {Sims, Robert J and Reinberg, Danny}, title = {Is there a code embedded in proteins that is based on post-translational modifications?}, journal = {Nat. Rev. Mol. Cell Biol.}, year = {2008}, volume = {9}, number = {10}, pages = {815--20}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18784729}, doi = {http://dx.doi.org/10.1038/nrm2502} }
SinRei06	Singla, V. & Reiter, J.F.	The primary cilium as the cell's antenna: signaling at a sensory organelle [Abstract] [BibTeX] [URL] [PDF]	2006	Science Vol. 313 (5787) , pp. 629-33	article	embryology, developmental
Abstract: Almost every vertebrate cell has a specialized cell surface projection called a primary cilium. Although these structures were first described more than a century ago, the full scope of their functions remains poorly understood. Here, we review emerging evidence that in addition to their well-established roles in sight, smell, and mechanosensation, primary cilia are key participants in intercellular signaling. This new appreciation of primary cilia as cellular antennae that sense a wide variety of signals could help explain why ciliary defects underlie such a wide range of human disorders, including retinal degeneration, polycystic kidney disease, Bardet-Biedl syndrome, and neural tube defects.
BibTeX: @article{SinRei06, author = {Singla, Veena and Reiter, Jeremy F}, title = {The primary cilium as the cell's antenna: signaling at a sensory organelle}, journal = {Science}, year = {2006}, volume = {313}, number = {5787}, pages = {629--33}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16888132}, doi = {http://dx.doi.org/10.1126/science.1124534} }
SonPfa05	Song, M. & Pfaff, S.	Hox genes: the instructors working at motor pools [BibTeX] [PDF]	2005	Cell Vol. 123 (3) , pp. 363-365	article	genetic
BibTeX: @article{SonPfa05, author = {Song, M.R. and Pfaff, S.L.}, title = {Hox genes: the instructors working at motor pools}, journal = {Cell}, publisher = {Elsevier}, year = {2005}, volume = {123}, number = {3}, pages = {363--365} }
SpiMir03	Spirin, V. & Mirny, L. a.	Protein complexes and functional modules in molecular networks [Abstract] [BibTeX] [URL] [PDF]	2003	Proc. Natl. Acad. Sci. U.S.A. Vol. 100 (21) , pp. 12123-8	article	metabolic, signalling
Abstract: Proteins, nucleic acids, and small molecules form a dense network of molecular interactions in a cell. Molecules are nodes of this network, and the interactions between them are edges. The architecture of molecular networks can reveal important principles of cellular organization and function, similarly to the way that protein structure tells us about the function and organization of a protein. Computational analysis of molecular networks has been primarily concerned with node degree [Wagner, A. & Fell, D. A. (2001) Proc. R. Soc. London Ser. B 268, 1803-1810; Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. (2000) Nature 407, 651-654] or degree correlation [Maslov, S. & Sneppen, K. (2002) Science 296, 910-913], and hence focused on single/two-body properties of these networks. Here, by analyzing the multibody structure of the network of protein-protein interactions, we discovered molecular modules that are densely connected within themselves but sparsely connected with the rest of the network. Comparison with experimental data and functional annotation of genes showed two types of modules: (i) protein complexes (splicing machinery, transcription factors, etc.) and (ii) dynamic functional units (signaling cascades, cell-cycle regulation, etc.). Discovered modules are highly statistically significant, as is evident from comparison with random graphs, and are robust to noise in the data. Our results provide strong support for the network modularity principle introduced by Hartwell et al. [Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. (1999) Nature 402, C47-C52], suggesting that found modules constitute the "building blocks" of molecular networks.
BibTeX: @article{SpiMir03, author = {Spirin, Victor and Mirny, Leonid a}, title = {Protein complexes and functional modules in molecular networks}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2003}, volume = {100}, number = {21}, pages = {12123--8}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=218723&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1073/pnas.2032324100} }
SpoTur02	Spotswood, H.; Turner, B. & others	An increasingly complex code [BibTeX] [PDF]	2002	Journal of Clinical Investigation Vol. 110 (5) , pp. 577-582	article	histone
BibTeX: @article{SpoTur02, author = {Spotswood, H.T. and Turner, B.M. and others}, title = {An increasingly complex code}, journal = {Journal of Clinical Investigation}, publisher = {Am Soc Clin Investig}, year = {2002}, volume = {110}, number = {5}, pages = {577--582} }
Ste08	Steitz, T. a.	A structural understanding of the dynamic ribosome machine [Abstract] [BibTeX] [URL] [PDF]	2008	Nat. Rev. Mol. Cell Biol. Vol. 9 (3) , pp. 242-53	article	rna
Abstract: Ribosomes, which are central to protein synthesis and convert transcribed mRNAs into polypeptide chains, have been the focus of structural and biochemical studies for more than 50 years. The structure of its larger subunit revealed that the ribosome is a ribozyme with RNA at the heart of its enzymatic activity that catalyses peptide bond formation. Numerous initiation, elongation and release factors ensure that protein synthesis occurs progressively and with high specificity. In the past few years, high-resolution structures have provided molecular snapshots of different intermediates in ribosome-mediated translation in atomic detail. Together, these studies have revolutionized our understanding of the mechanism of protein synthesis.
BibTeX: @article{Ste08, author = {Steitz, Thomas a}, title = {A structural understanding of the dynamic ribosome machine}, journal = {Nat. Rev. Mol. Cell Biol.}, year = {2008}, volume = {9}, number = {3}, pages = {242--53}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18292779}, doi = {http://dx.doi.org/10.1038/nrm2352} }
StoDroBre06	Stolovicki, E.; Dror, T.; Brenner, N. & Braun, E.	Synthetic gene recruitment reveals adaptive reprogramming of gene regulation in yeast [Abstract] [BibTeX] [URL] [PDF]	2006	Genetics Vol. 173 (1) , pp. 75-85	article	epigenetic
Abstract: The recruitment of a gene to a foreign regulatory system is a major evolutionary event that can lead to novel phenotypes. However, the evolvability potential of cells depends on their ability to cope with challenges presented by gene recruitment. To study this ability, we combined synthetic gene recruitment with continuous culture and online measurements of the metabolic and regulatory dynamics over long timescales. The gene HIS3 from the histidine synthesis pathway was recruited to the GAL system, responsible for galactose utilization in the yeast S. cerevisiae. Following a switch from galactose to glucose--from induced to repressed conditions of the GAL system--in histidine-lacking chemostats (where the recruited HIS3 is essential), the regulatory system reprogrammed to adaptively tune HIS3 expression, allowing the cells to grow competitively in pure glucose. The adapted state was maintained for hundreds of generations in various environments. The timescales involved and the reproducibility of separate experiments render spontaneous mutations an unlikely underlying mechanism. Essentially all cells could adapt, excluding selection over a genetically variable population. The results reveal heritable adaptation induced by the exposure to glucose. They demonstrate that genetic regulatory networks have the potential to support highly demanding events of gene recruitment.
BibTeX: @article{StoDroBre06, author = {Stolovicki, Elad and Dror, Tali and Brenner, Naama and Braun, Erez}, title = {Synthetic gene recruitment reveals adaptive reprogramming of gene regulation in yeast}, journal = {Genetics}, year = {2006}, volume = {173}, number = {1}, pages = {75--85}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1461455&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1534/genetics.106.055442} }
StoKuf08	Storchova, Z. & Kuffer, C.	The consequences of tetraploidy and aneuploidy [Abstract] [BibTeX] [URL] [PDF]	2008	J. Cell Sci. Vol. 121 (Pt 23) , pp. 3859-66	article	genetic
Abstract: Polyploidy, an increased number of chromosome sets, is a surprisingly common phenomenon in nature, particularly in plants and fungi. In humans, polyploidy often occurs in specific tissues as part of terminal differentiation. Changes in ploidy can also result from pathophysiological events that are caused by viral-induced cell fusion or erroneous cell division. Tetraploidization can initiate chromosomal instability (CIN), probably owing to supernumerary centrosomes and the doubled chromosome mass. CIN, in turn, might persist or soon give way to a stably propagating but aneuploid karyotype. Both CIN and stable aneuploidy are commonly observed in cancers. Recently, it has been proposed that an increased number of chromosome sets can promote cell transformation and give rise to an aneuploid tumor. Here, we review how tetraploidy can occur and describe the cellular responses to increased ploidy. Furthermore, we discuss how the specific physiological changes that are triggered by polyploidization might be used as novel targets for cancer therapy.
BibTeX: @article{StoKuf08, author = {Storchova, Zuzana and Kuffer, Christian}, title = {The consequences of tetraploidy and aneuploidy}, journal = {J. Cell Sci.}, year = {2008}, volume = {121}, number = {Pt 23}, pages = {3859--66}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19020304}, doi = {http://dx.doi.org/10.1242/jcs.039537} }
Sto06	Stotz, K.	With 'genes' like that, who needs an environment? Postgenomics's argument for the 'ontogeny of information' [BibTeX] [PDF]	2006	Philos. Sci. Vol. 73 , pp. 905-917	article	interpreting cell
BibTeX: @article{Sto06, author = {Stotz, Karola}, title = {With 'genes' like that, who needs an environment? Postgenomics's argument for the 'ontogeny of information'}, journal = {Philos. Sci.}, year = {2006}, volume = {73}, pages = {905--917} }
TejVal10	Tejedor, J.R. & Valcárcel, J.	Breaking the second genetic code [BibTeX] [PDF]	2010	Nature Vol. 465 , pp. 45-46	article	genetic
BibTeX: @article{TejVal10, author = {Tejedor, J Ramón and Valcárcel, Juan}, title = {Breaking the second genetic code}, journal = {Nature}, year = {2010}, volume = {465}, pages = {45--46} }
Tom75	Tomkins, G.M.	The metabolic code [BibTeX] [PDF]	1975	Science Vol. 189 , pp. 760-763	article	metabolic, signalling
BibTeX: @article{Tom75, author = {Tomkins, G. M.}, title = {The metabolic code}, journal = {Science}, year = {1975}, volume = {189}, pages = {760--763} }
TooReb05	Tootle, T.L. & Rebay, I.	Post-translational modifications influence transcription factor activity: a view from the ETS superfamily [Abstract] [BibTeX] [URL] [PDF]	2005	BioEssays Vol. 27 (3) , pp. 285-98	article	metabolic, signalling
Abstract: Transcription factors provide nodes of information integration by serving as nuclear effectors of multiple signaling cascades, and thus elaborate layers of regulation, often involving post-translational modifications, modulating and coordinate activities. Such modifications can rapidly and reversibly regulate virtually all transcription factor functions, including subcellular localization, stability, interactions with cofactors, other post-translational modifications and transcriptional activities. Aside from analyses of the effects of serine/threonine phosphorylation, studies on post-translational modifications of transcription factors are only in the initial stages. In particular, the regulatory possibilities afforded by combinatorial usage of and competition between distinct modifications on an individual protein are immense, and with respect to large families of closely related transcription factors, offer the potential of conferring critical specificity. Here we will review the post-translational modifications known to regulate ETS transcriptional effectors and will discuss specific examples of how such modifications influence their activities to highlight emerging paradigms in transcriptional regulation.
BibTeX: @article{TooReb05, author = {Tootle, Tina L and Rebay, Ilaria}, title = {Post-translational modifications influence transcription factor activity: a view from the ETS superfamily}, journal = {BioEssays}, year = {2005}, volume = {27}, number = {3}, pages = {285--98}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15714552}, doi = {http://dx.doi.org/10.1002/bies.20198} }
TsuEnsMor94	Tsuchida, T.; Ensini, M.; Morton, S.B.; Baldassare, M.; Edlund, T.; Jessell, T.M. & Pfaff, S.L.	Topographic organization of embryonic motor neurons defined by expression of LIM homeobox gene [BibTeX] [PDF]	1994	Cell Vol. 79 , pp. 957-970	article	embryology, developmental
BibTeX: @article{TsuEnsMor94, author = {Tsuchida, T and Ensini, M and Morton, S B and Baldassare, M and Edlund, T and Jessell, T M and Pfaff, S L}, title = {Topographic organization of embryonic motor neurons defined by expression of LIM homeobox gene}, journal = {Cell}, year = {1994}, volume = {79}, pages = {957--970} }
Tur02	Turner, B.	Cellular memory and the histone code [BibTeX] [PDF]	2002	Cell Vol. 111 (3) , pp. 285-291	article	histone
BibTeX: @article{Tur02, author = {Turner, B.M.}, title = {Cellular memory and the histone code}, journal = {Cell}, publisher = {Elsevier}, year = {2002}, volume = {111}, number = {3}, pages = {285--291} }
Tur00	Turner, B.	Histone acetylation and an epigenetic code [BibTeX] [PDF]	2000	Bioessays Vol. 22 (9) , pp. 836-845	article
BibTeX: @article{Tur00, author = {Turner, B.M.}, title = {Histone acetylation and an epigenetic code}, journal = {Bioessays}, publisher = {Wiley Online Library}, year = {2000}, volume = {22}, number = {9}, pages = {836--845} }
Tur07	Turner, B.M.	Defining an epigenetic code [BibTeX] [PDF]	2007	Nat. Cell Biol. Vol. 9 , pp. 2-6	article	histone
BibTeX: @article{Tur07, author = {Turner, Bryan M}, title = {Defining an epigenetic code}, journal = {Nat. Cell Biol.}, year = {2007}, volume = {9}, pages = {2--6} }
VerGae07	Verhey, K.J. & Gaertig, J.	The tubulin code [BibTeX] [PDF]	2007	Cell Cycle Vol. 6 (17) , pp. 2152-2160	article	cytoskeletal
BibTeX: @article{VerGae07, author = {Verhey, Kristen J and Gaertig, Jacek}, title = {The tubulin code}, journal = {Cell Cycle}, year = {2007}, volume = {6}, number = {17}, pages = {2152--2160} }
VuJirHof06	Vu, T.H.; Jirtle, R.L. & Hoffman, a.R.	Cross-species clues of an epigenetic imprinting regulatory code for the IGF2R gene [Abstract] [BibTeX] [URL] [PDF]	2006	Cytogenet. Genome Res. Vol. 113 (1-4) , pp. 202-8	article	epigenetic
Abstract: The epigenetic marks on the IGF2R gene that encodes a receptor responsible for IGF-II degradation consist of differentially methylated DNA in association with multiple modifications on the associated histones. We review these epigenetic marks across various species during the evolution of IGF2R imprinting. Both IGF2 and IGF2R genesare imprinted in the mammal lineage that diverged from Monotremata approximately 150 million years ago. While IGF2 is consistently imprinted in all mammals following its divergence, IGF2R imprinting disappears in the Euarchonta lineage, including human species, approximately 75 million years ago. Differential DNA methylation marks on the two parental alleles correlate with imprinting in all imprinted genes including IGF2R. While the DNA methylation marks in the IGF2R promoter region 1 (DMR1) correlate with IGF2R allelic expression, the DNA methylation marks in the intron region 2 (DMR2) fail to correlate with IGF2R imprinting status in a number of species. Human IGF2R and mouse neuronal Igf2r are not imprinted despite the presence of DMR2. We have noted that human IGF2R is not imprinted in more than 100 informative samples including various tumor tissues. Furthermore, opossum (Marsupialia) IGF2R is consistently imprinted despite the absence of DMR2. These lines of evidence indicate that DNA methylation marks in DMR2 are neither necessary nor sufficient for consistent imprinting of IGF2R across species. Histone modification marks, however, correlate more consistently with the tissue-specific and species-specific imprinting status of IGF2R in human and mouse. Acetylated histone H3 and H4 and methylated lysine 4 of H3 (H3-K4Me) associate with transcriptionally active alleles while tri-methylated lysine 9 of H3 (H3-K9Me3) marks the silenced alleles. In the mouse, an antisense non-coding transcript called Air is transcribed from DMR2 on the paternal allele, and this imprinted transcript plays a central role in Igf2r imprinting. Mouse Igf2r imprinting depends on an Air RNA while the existence of AIR in other species is unknown. Overall, DNA methylation, histone acetylation, and histone methylation play a vital role in coordinating IGF2R allelic expression across all species. Rare monoallelic or skewed allelic expression of human IGF2R and their biological importance warrants further rigorous study.
BibTeX: @article{VuJirHof06, author = {Vu, T H and Jirtle, R L and Hoffman, a R}, title = {Cross-species clues of an epigenetic imprinting regulatory code for the IGF2R gene}, journal = {Cytogenet. Genome Res.}, year = {2006}, volume = {113}, number = {1-4}, pages = {202--8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16575181}, doi = {http://dx.doi.org/10.1159/000090833} }
WagLyn08	Wagner, G.P. & Lynch, V.J.	The gene regulatory logic of transcription factor evolution [Abstract] [BibTeX] [URL] [PDF]	2008	Trends Ecol. Evol. Vol. 23 (7) , pp. 377-85	article	epigenetic
Abstract: A growing debate in evolutionary and developmental biology concerns the relative contribution of cis-regulatory and protein (particularly transcription factor) changes to developmental evolution. Central to this argument are the perceived conservation of transcription factor functions and the modular architecture of cis-regulatory elements. In this paper, we review recent studies on transcription factor proteins that show that transcription factor genes undergo adaptive evolution and evolve novel functions that contribute to the evolution of development. Furthermore, we review experimental work that shows that transcription factor proteins are modular and can evolve with minimal pleiotropic effects. We conclude that changes in the function of proteins are likely directly contributing to developmental evolution.
BibTeX: @article{WagLyn08, author = {Wagner, Günter P and Lynch, Vincent J}, title = {The gene regulatory logic of transcription factor evolution}, journal = {Trends Ecol. Evol.}, year = {2008}, volume = {23}, number = {7}, pages = {377--85}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18501470}, doi = {http://dx.doi.org/10.1016/j.tree.2008.03.006} }
WanSonWan09	Wang, G.G.; Song, J.; Wang, Z.; Dormann, H.L.; Casadio, F.; Li, H.; Luo, J.-L.; Patel, D.J. & Allis, C.D.	Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger [Abstract] [BibTeX] [URL] [PDF]	2009	Nature Vol. 459 (7248) , pp. 847-51	article	histone
Abstract: Histone H3 lysine 4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98-PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development.
BibTeX: @article{WanSonWan09, author = {Wang, Gang G and Song, Jikui and Wang, Zhanxin and Dormann, Holger L and Casadio, Fabio and Li, Haitao and Luo, Jun-Li and Patel, Dinshaw J and Allis, C David}, title = {Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger}, journal = {Nature}, publisher = {Nature Publishing Group}, year = {2009}, volume = {459}, number = {7248}, pages = {847--51}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2697266&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1038/nature08036} }
WatDanGor09	Watts, J.M.; Dang, K.K.; Gorelick, R.J.; Leonard, C.W.; Bess, J.W.; Swanstrom, R.; Burch, C.L. & Weeks, K.M.	Architecture and secondary structure of an entire HIV-1 RNA genome [Abstract] [BibTeX] [URL] [PDF]	2009	Nature Vol. 460 (7256) , pp. 711-6	article	genetic
Abstract: Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests that RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions, including splice site acceptors and hypervariable regions. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code.
BibTeX: @article{WatDanGor09, author = {Watts, Joseph M and Dang, Kristen K and Gorelick, Robert J and Leonard, Christopher W and Bess, Julian W and Swanstrom, Ronald and Burch, Christina L and Weeks, Kevin M}, title = {Architecture and secondary structure of an entire HIV-1 RNA genome}, journal = {Nature}, publisher = {Nature Publishing Group}, year = {2009}, volume = {460}, number = {7256}, pages = {711--6}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2724670&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1038/nature08237} }
Wei05	Weiss, K.M.	The phenogenetic logic of life [Abstract] [BibTeX] [URL] [PDF]	2005	Nat. Rev. Genet. Vol. 6 (1) , pp. 36-45	article	brain transcription
Abstract: For nearly a century we have understood that life works through genes, and so have had an elegant theory for general evolution. But this did not explain the kinds of traits that characterize organisms, nor how genes produce them. Advances in recent decades have opened the way for an understanding of the phenogenetic logic or relational principles of life, by which a few basic characteristics of genomes produce biological phenotypes through some basic developmental processes. This logic provides a general explanation of the nature and source of organismal design, and a powerful programme for research.
BibTeX: @article{Wei05, author = {Weiss, Kenneth M}, title = {The phenogenetic logic of life}, journal = {Nat. Rev. Genet.}, year = {2005}, volume = {6}, number = {1}, pages = {36--45}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15630420}, doi = {http://dx.doi.org/10.1038/nrg1502} }
Wil09	Wills, P.R.	Informed generation: physical origin and biological evolution of genetic codescript interpreters [Abstract] [BibTeX] [URL] [PDF]	2009	J. Theor. Biol. Vol. 257 (3) , pp. 345-58	article	interpreting cell
Abstract: The information stored in the genome of an organism has long been thought of in computational terms as a kind of codescript for the construction, operation and control of the system in which it is found. However, genomic sequence information can be interpreted as biological instructions and executed as a genetic codescript only by a suitably prepared cell with which the program is in proper registration. We enquire into the character of the evolutionary process that generates physical systems capable of interpreting, in increasingly elaborate ways, the genetic information they contain. The principle of Informed Generation specifies the need for the spontaneous emergence and evolutionary development of self-organizing processes that generate phenotypes from genotypes. The principle of Informed Generation describes a ubiquitous feature of biological systems: without the prior existence of certain components or functionalities, which are required for the production of themselves and others, no configuration of genetic information that accumulated through Natural Selection could ever serve as a codescript for an organism. The operation of Informed Generation is demonstrated in the stepwise evolution of genetic coding and the general distinction between Natural Selection and Informed Generation is illustrated through consideration of gene-replicase-translatase (GRT) system. It is proposed that Informed Generation represents a quite general process of evolutionary self-organization in biological systems whereby essentially irreversible transitions in the systems' dynamics take them to historically contingent, isolated states whose characteristics are determinants of biological specificity. The operation of Informed Generation may have left detectable traces in topographical features of complex intracellular and ecological networks.
BibTeX: @article{Wil09, author = {Wills, Peter R}, title = {Informed generation: physical origin and biological evolution of genetic codescript interpreters}, journal = {J. Theor. Biol.}, year = {2009}, volume = {257}, number = {3}, pages = {345--58}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19174168}, doi = {http://dx.doi.org/10.1016/j.jtbi.2008.12.030} }
WraAbo98	Wray, G.A. & Abouheif, E.	When is homology not homology? [BibTeX] [PDF]	1998	Curr. Opin. Genet. Dev. Vol. 8 , pp. 675-680	article	embryology, developmental
BibTeX: @article{WraAbo98, author = {Wray, Gregory A and Abouheif, Ehab}, title = {When is homology not homology?}, journal = {Curr. Opin. Genet. Dev.}, year = {1998}, volume = {8}, pages = {675--680} }
XinZhoSon07	Xin, L.; Zhou, G.-L.; Song, W.; Wu, X.-S.; Wei, G.-H.; Hao, D.-L.; Lv, X.; Liu, D.-P. & Liang, C.-C.	Exploring cellular memory molecules marking competent and active transcriptions [Abstract] [BibTeX] [URL] [PDF]	2007	BMC Mol. Biol. Vol. 8 , pp. 31	article	histone
Abstract: Development in higher eukaryotes involves programmed gene expression. Cell type-specific gene expression is established during this process and is inherited in succeeding cell cycles. Higher eukaryotes have evolved elegant mechanisms by which committed gene-expression states are transmitted through numerous cell divisions. Previous studies have shown that both DNase I-sensitive sites and the basal transcription factor TFIID remain on silenced mitotic chromosomes, suggesting that certain trans-factors might act as bookmarks, maintaining the information and transmitting it to the next generation.
BibTeX: @article{XinZhoSon07, author = {Xin, Li and Zhou, Guo-Ling and Song, Wei and Wu, Xue-Song and Wei, Gong-Hong and Hao, De-Long and Lv, Xiang and Liu, De-Pei and Liang, Chih-Chuan}, title = {Exploring cellular memory molecules marking competent and active transcriptions}, journal = {BMC Mol. Biol.}, year = {2007}, volume = {8}, pages = {31}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1884170&tool=pmcentrez&rendertype=abstract}, doi = {http://dx.doi.org/10.1186/1471-2199-8-31} }
ZacGliTza07	Zacharioudakis, I.; Gligoris, T. & Tzamarias, D.	A yeast catabolic enzyme controls transcriptional memory [Abstract] [BibTeX] [URL] [PDF]	2007	Curr. Biol. Vol. 17 (23) , pp. 2041-6	article	metabolic, signalling
Abstract: It has been postulated that chromatin modifications can persist through mitosis and meiosis, thereby securing memory of transcriptional states. Whether these chromatin marks can self-propagate in progeny independently of relevant trans-acting factors is an important question in phenomena related to epigenesis. "Adaptive cellular memory" displayed by yeast cells offers a convenient system to address this question. The yeast GAL genes are slowly activated by Gal4 when cells are first exposed to galactose, but their progeny, grown in glucose media, exhibit a fast activation mode upon re-exposure to this sugar. This "galactose memory" persists for several generations and was recently proposed to involve chromatin modifications and perinuclear topology of the GAL genes cluster. Here, we perform a heterokaryon assay demonstrating that this memory does not have a chromatin basis but is maintained by cytoplasmic factor(s) produced upon previous galactose induction. We show that Gal3, the cytoplasmic rate-limiting factor that releases the Gal4 activator, is dispensable for preserving galactose memory. Instead, the important memory determinant is a close Gal3 homolog, the highly expressed Gal1 galactokinase, the residual activity of which preserves memory in progeny cells by rapidly turning on the Gal4 activator upon cells' re-exposure to galactose.
BibTeX: @article{ZacGliTza07, author = {Zacharioudakis, Ioannis and Gligoris, Thomas and Tzamarias, Dimitris}, title = {A yeast catabolic enzyme controls transcriptional memory}, journal = {Curr. Biol.}, year = {2007}, volume = {17}, number = {23}, pages = {2041--6}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17997309}, doi = {http://dx.doi.org/10.1016/j.cub.2007.10.044} }
ZhaMoqRat10	Zhang, Y.; Moqtaderi, Z.; Rattner, B.P.; Euskirchen, G.; Snyder, M.; Kadonaga, J.T.; Liu, X.S. & Struhl, K.	Evidence against a genomic code for nucleosome positioning? [BibTeX] [URL] [PDF]	2010	Nat. Struct. Mol. Biol. Vol. 17 (8) , pp. 920-923	article	nucleosome
BibTeX: @article{ZhaMoqRat10, author = {Zhang, Yong and Moqtaderi, Zarmik and Rattner, Barbara P and Euskirchen, Ghia and Snyder, Michael and Kadonaga, James T and Liu, X Shirley and Struhl, Kevin}, title = {Evidence against a genomic code for nucleosome positioning?}, journal = {Nat. Struct. Mol. Biol.}, year = {2010}, volume = {17}, number = {8}, pages = {920--923}, url = {http://www.nature.com/doifinder/10.1038/nsmb0810-920}, doi = {http://dx.doi.org/10.1038/nsmb0810-920} }

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