The selection and function of cell type-specific enhancers

S Heinz, CE Romanoski, C Benner… - Nature reviews Molecular …, 2015 - nature.com
The human body contains several hundred cell types, all of which share the same genome.
In metazoans, much of the regulatory code that drives cell type-specific gene expression is …

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 …

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

T Gao, J Qian - Nucleic acids research, 2020 - academic.oup.com
Enhancers are distal cis-regulatory elements that activate the transcription of their target
genes. They regulate a wide range of important biological functions and processes …

[HTML][HTML] A high-resolution map of human enhancer RNA loci characterizes super-enhancer activities in cancer

H Chen, H Liang - Cancer cell, 2020 - cell.com
Although enhancers play critical roles in cancer, quantifying enhancer activities in clinical
samples remains challenging, especially for super-enhancers. Enhancer activities can be …

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

J Mieczkowski, A Cook, SK Bowman, B Mueller… - Nature …, 2016 - nature.com
Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome
placement, usually measured by quantifying protection of DNA from enzymatic digestion …

Genomic methods in profiling DNA accessibility and factor localization

DC Klein, SJ Hainer - Chromosome Research, 2020 - Springer
Recent advancements in next-generation sequencing technologies and accompanying
reductions in cost have led to an explosion of techniques to examine DNA accessibility and …

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

AC Daugherty, RW Yeo, JD Buenrostro… - Genome …, 2017 - genome.cshlp.org
Chromatin accessibility, a crucial component of genome regulation, has primarily been
studied in homogeneous and simple systems, such as isolated cell populations or early …

Brd4's bromodomains mediate histone H3 acetylation and chromatin remodeling in pluripotent cells through P300 and Brg1

T Wu, YF Kamikawa, ME Donohoe - Cell reports, 2018 - cell.com
The pluripotent state of embryonic stem cells (ESCs) is defined by its transcriptome and
epigenome. The chromatin reader Brd4 determines ESC identity. Although Brd4 regulation …

[HTML][HTML] Insights into nucleosome organization in mouse embryonic stem cells through chemical map**

LN Voong, L **
S Brahma, S Henikoff - Trends in biochemical sciences, 2020 - cell.com
Gene regulation in eukaryotes requires the controlled access of sequence-specific
transcription factors (TFs) to their sites in a chromatin landscape dominated by …