Journal ArticleDOI
Histone modification: cause or cog?
Steven Henikoff,Ali Shilatifard +1 more
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TLDR
It is suggested that the 35-year-old DNA accessibility paradigm provides a mechanistically sound basis for understanding the role of nucleosomes in gene regulation and epigenetic inheritance and contributes to diversification of a chromatin landscape shaped by dynamic processes that are driven primarily by transcription and nucleosome remodeling.About:
This article is published in Trends in Genetics.The article was published on 2011-10-01. It has received 435 citations till now. The article focuses on the topics: Histone code & Chromatin remodeling.read more
Citations
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Journal ArticleDOI
Epigenetics and the environment: emerging patterns and implications.
TL;DR: Although the underlying mechanisms remain largely unknown, particularly in humans, mechanistic insights are emerging from experimental model systems, which have implications for structuring future research and understanding disease and development.
Journal ArticleDOI
Regulation of nucleosome dynamics by histone modifications
TL;DR: Property of the major types of histone modification in the context of their associated biological processes are considered to view them in light of the cellular mechanisms that regulate nucleosome dynamics.
Journal ArticleDOI
Molecular mechanisms and potential functions of histone demethylases.
TL;DR: The biochemical activities of these histone demethylases towards specific Lys residues on histones, and in some cases non-histone substrates, have highlighted their importance in developmental control, cell-fate decisions and disease.
Journal ArticleDOI
Defining functional DNA elements in the human genome
Manolis Kellis,Barbara J. Wold,Michael Snyder,Bradley E. Bernstein,Anshul Kundaje,Georgi K. Marinov,Lucas D. Ward,Ewan Birney,Gregory E. Crawford,Job Dekker,Ian Dunham,Laura Elnitski,Peggy J. Farnham,Elise A. Feingold,Mark Gerstein,Morgan C. Giddings,David M. Gilbert,Thomas R. Gingeras,Eric D. Green,Roderic Guigó,Tim Hubbard,Jim Kent,Jason D. Lieb,Richard M. Myers,Michael J. Pazin,Bing Ren,John A. Stamatoyannopoulos,Zhiping Weng,Kevin P. White,Ross C. Hardison +29 more
TL;DR: The strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies are reviewed.
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Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put.
TL;DR: The stage is now set to reveal fundamental epigenetic mechanisms that determine how Polycomb target genes are silenced and howPolycomb silence is preserved through cell-cycle progression.
References
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Journal ArticleDOI
The language of covalent histone modifications.
Brian D. Strahl,C D Allis +1 more
TL;DR: It is proposed that distinct histone modifications, on one or more tails, act sequentially or in combination to form a ‘histone code’ that is, read by other proteins to bring about distinct downstream events.
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Combinatorial patterns of histone acetylations and methylations in the human genome
Zhibin Wang,Chongzhi Zang,Jeffrey A. Rosenfeld,Jeffrey A. Rosenfeld,Dustin E. Schones,Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Weiqun Peng,Michael Q. Zhang,Keji Zhao +11 more
TL;DR: The data suggest that a large number of histone modifications may act cooperatively to prepare chromatin for transcriptional activation and be associated with promoters and enhancers.
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A unique chromatin signature uncovers early developmental enhancers in humans
Alvaro Rada-Iglesias,Ruchi Bajpai,Tomek Swigut,Samantha A. Brugmann,Ryan A. Flynn,Joanna Wysocka +5 more
TL;DR: It is demonstrated that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements.
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Cytosine methylation and the ecology of intragenomic parasites
TL;DR: It has become increasingly difficult to hold that reversible promoter methylation is commonly involved in developmental gene control; instead, suppression of parasitic sequence elements appears to be the primary function of cytosine methylation, with crucial secondary roles in allele-specific gene expression as seen in X inactivation and genomic imprinting.
PatentDOI
Genome-wide location and function of dna binding proteins
TL;DR: In this paper, a method for identifying a set of genes where cell cycle regulator binding correlates with gene expression and identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.