Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers

Epigenetics : Official Journal of the DNA Methylation Society
Aziz KhanXuegong Zhang

Abstract

Super-enhancers and stretch enhancers represent classes of transcriptional enhancers that have been shown to control the expression of cell identity genes and carry disease- and trait-associated variants. Specifically, super-enhancers are clusters of enhancers defined based on the binding occupancy of master transcription factors, chromatin regulators, or chromatin marks, while stretch enhancers are large chromatin-defined regulatory regions of at least 3,000 base pairs. Several studies have characterized these regulatory regions in numerous cell types and tissues to decipher their functional importance. However, the differences and similarities between these regulatory regions have not been fully assessed. We integrated genomic, epigenomic, and transcriptomic data from ten human cell types to perform a comparative analysis of super and stretch enhancers with respect to their chromatin profiles, cell type-specificity, and ability to control gene expression. We found that stretch enhancers are more abundant, more distal to transcription start sites, cover twice as much the genome, and are significantly less conserved than super-enhancers. In contrast, super-enhancers are significantly more enriched for active chromatin marks and...Continue Reading

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Citations

May 10, 2019·Cancers·Feda H Hamdan, Steven A Johnsen
Jun 21, 2019·Journal of Cellular Biochemistry·Vahideh AhmadzadehHabib Zarredar
Jul 18, 2019·Journal of Hematology & Oncology·Yunlu JiaJianbiao Zhou
Jul 14, 2019·Journal of Muscle Research and Cell Motility·Fiona C Wardle
Dec 28, 2019·International Journal of Molecular Sciences·Hironori Matsuyama, Hiroshi I Suzuki
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Jun 4, 2020·Cell Reports·Hiroki MichidaMariko Okada-Hatakeyama
Jul 29, 2021·Nucleic Acids Research·Isidore MushimiyimanaNihay Laham-Karam
Oct 14, 2020·Journal of Molecular Cell Biology·Pixi YanXiaohua Shen
Aug 31, 2021·EBioMedicine·Jared M AndrewsJacqueline E Payton

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
acetylation
ChIP-seq
RNA-seq
K562

Software Mentioned

BEDTools
GREAT
GRO
R
. plot
seq
bowtie2
Intervene
ngs
Biodalliance genome browser

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