Journal ArticleDOI
Determinants and dynamics of genome accessibility
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TLDR
The interplay of nucleosome packaging and chromatin access contributes to the regulation of transcription, replication and repair in eukaryotes is discussed by reviewing the current understanding.Abstract:
In eukaryotes, all DNA-templated reactions occur in the context of chromatin. Nucleosome packaging inherently restricts DNA accessibility for regulatory proteins but also provides an opportunity to regulate DNA-based processes through modulating nucleosome positions and local chromatin structure. Recent advances in genome-scale methods are yielding increasingly detailed profiles of the genomic distribution of nucleosomes, their modifications and their modifiers. The picture now emerging is one in which the dynamic control of genome accessibility is governed by contributions from DNA sequence, ATP-dependent chromatin remodelling and nucleosome modifications. Here we discuss the interplay of these processes by reviewing our current understanding of how chromatin access contributes to the regulation of transcription, replication and repair.read more
Citations
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Journal ArticleDOI
The accessible chromatin landscape of the human genome
Robert E. Thurman,Eric Rynes,Richard Humbert,Jeff Vierstra,Matthew T. Maurano,Eric Haugen,Nathan C. Sheffield,Andrew B. Stergachis,Hao Wang,Benjamin Vernot,Kavita Garg,Sam John,Richard Sandstrom,Daniel Bates,Lisa Boatman,Theresa K. Canfield,Morgan Diegel,Douglas Dunn,Abigail K. Ebersol,Tristan Frum,Erika Giste,Audra K. Johnson,Ericka M. Johnson,Tanya Kutyavin,Bryan R. Lajoie,Bum Kyu Lee,Kristen Lee,Darin London,Dimitra Lotakis,Shane Neph,Fidencio Neri,Eric D. Nguyen,Hongzhu Qu,Hongzhu Qu,Alex Reynolds,Vaughn Roach,Alexias Safi,Minerva E. Sanchez,Amartya Sanyal,Anthony Shafer,Jeremy M. Simon,Lingyun Song,Shinny Vong,Molly Weaver,Yongqi Yan,Zhancheng Zhang,Zhuzhu Zhang,Boris Lenhard,Muneesh Tewari,Michael O. Dorschner,R. Scott Hansen,Patrick A. Navas,George Stamatoyannopoulos,Vishwanath R. Iyer,Jason D. Lieb,Shamil R. Sunyaev,Joshua M. Akey,Peter J. Sabo,Rajinder Kaul,Terrence S. Furey,Job Dekker,Gregory E. Crawford,John A. Stamatoyannopoulos,John A. Stamatoyannopoulos +63 more
TL;DR: The first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types is presented, revealing novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns.
Journal ArticleDOI
ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide
TL;DR: This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin, which can be used to infer regions of increased accessibility, as well as to map regions of transcription‐factor binding and nucleosome position.
Journal ArticleDOI
Regulation of type I interferon responses
TL;DR: In this paper, the authors summarize the signalling and epigenetic mechanisms that regulate type I IFN-induced STAT activation and ISG transcription and translation and conclude that these regulatory mechanisms determine the biological outcomes of type I ILN responses and whether pathogens are cleared effectively or chronic infection or autoimmune disease ensues.
Journal ArticleDOI
Transcription factors: from enhancer binding to developmental control.
TL;DR: Current knowledge of transcription factor function from genomic and genetic studies is reviewed and how different strategies, including extensive cooperative regulation, progressive priming of regulatory elements, and the integration of activities from multiple enhancers, confer specificity and robustness to transcriptional regulation during development are discussed.
Journal ArticleDOI
Histone methylation: a dynamic mark in health, disease and inheritance
Eric L. Greer,Yang Shi +1 more
TL;DR: This work provides a broad overview of how histone methylation is regulated and leads to biological outcomes and suggests its links to disease and ageing and possibly to transmission of traits across generations are illustrated.
References
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Journal ArticleDOI
Chromatin Modifications and Their Function
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Journal ArticleDOI
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Journal ArticleDOI
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TL;DR: The purification and characterization of an EED-EZH2 complex, the human counterpart of the Drosophila ESC-E(Z) complex, is reported, and it is demonstrated that the complex specifically methylates nucleosomal histone H3 at lysine 27 (H3-K27).
Journal ArticleDOI
Capturing Chromosome Conformation
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Journal ArticleDOI
The Role of Chromatin during Transcription
TL;DR: This Review highlights advances in the understanding of chromatin regulation and discusses how such regulation affects the binding of transcription factors as well as the initiation and elongation steps of transcription.