Chromatin accessibility and the regulatory epigenome

SL Klemm, Z Shipony, WJ Greenleaf - Nature Reviews Genetics, 2019 - nature.com
Physical access to DNA is a highly dynamic property of chromatin that plays an essential
role in establishing and maintaining cellular identity. The organization of accessible …

Mechanisms of enhancer action: the known and the unknown

A Panigrahi, BW O'Malley - Genome biology, 2021 - Springer
Differential gene expression mechanisms ensure cellular differentiation and plasticity to
shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential …

Ever-changing landscapes: transcriptional enhancers in development and evolution

HK Long, SL Prescott, J Wysocka - Cell, 2016 - cell.com
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating
spatiotemporally precise gene-expression programs during development. Consequently …

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

K Adelman, JT Lis - Nature Reviews Genetics, 2012 - nature.com
Recent years have witnessed a sea change in our understanding of transcription regulation:
whereas traditional models focused solely on the events that brought RNA polymerase II …

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng… - Science, 2010 - science.org
We systematically generated large-scale data sets to improve genome annotation for the
nematode Caenorhabditis elegans, a key model organism. These data sets include …

AP-1 transcription factors and the BAF complex mediate signal-dependent enhancer selection

T Vierbuchen, E Ling, CJ Cowley, CH Couch, X Wang… - Molecular cell, 2017 - cell.com
Enhancer elements are genomic regulatory sequences that direct the selective expression
of genes so that genetically identical cells can differentiate and acquire the highly …

The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation

M Iwafuchi-Doi, G Donahue, A Kakumanu, JA Watts… - Molecular cell, 2016 - cell.com
Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding
of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind …

Chromatin accessibility profiling methods

L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

[HTML][HTML] Endothelial cells are central orchestrators of cytokine amplification during influenza virus infection

JR Teijaro, KB Walsh, S Cahalan, DM Fremgen… - Cell, 2011 - cell.com
Cytokine storm during viral infection is a prospective predictor of morbidity and mortality, yet
the cellular sources remain undefined. Here, using genetic and chemical tools to probe …

Determinants of nucleosome organization in primary human cells

A Valouev, SM Johnson, SD Boyd, CL Smith, AZ Fire… - Nature, 2011 - nature.com
Nucleosomes are the basic packaging units of chromatin, modulating accessibility of
regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate …