Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes

6Citations
Citations of this article
17Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

The term 'super enhancers' (SE) has been widely used to describe stretches of closely localized enhancers that are occupied collectively by large numbers of transcription factors (TFs) and co-factors, and control the transcription of highly-expressed genes. Through integrated analysis of >600 DNase-seq, ChIP-seq, GRO-seq, STARR-seq, RNA-seq, Hi-C and ChIA-PET data in five human cancer cell lines, we identified a new class of autonomous SEs (aSEs) that are excluded from classic SE calls by the widely used Rank Ordering of Super-Enhancers (ROSE) method. TF footprint analysis revealed that compared to classic SEs and regular enhancers, aSEs are tightly bound by a dense array of master lineage TFs, which serve as anchors to recruit additional TFs and co-factors in trans. In addition, aSEs are preferentially enriched for Cohesins, which likely involve in stabilizing long-distance interactions between aSEs and their distal target genes. Finally, we showed that aSEs can be reliably predicted using a single DNase-seq data or combined with Mediator and/or P300 ChIP-seq. Overall, our study demonstrates that aSEs represent a unique class of functionally important enhancer elements that distally regulate the transcription of highly expressed genes.

References Powered by Scopus

The Sequence Alignment/Map format and SAMtools

41111Citations
N/AReaders
Get full text

Fast and accurate short read alignment with Burrows-Wheeler transform

34835Citations
N/AReaders
Get full text

An integrated encyclopedia of DNA elements in the human genome

12925Citations
N/AReaders
Get full text

Cited by Powered by Scopus

Super-enhancer-driven lncRNA LIMD1-AS1 activated by CDK7 promotes glioma progression

12Citations
N/AReaders
Get full text

Integrated genomics approaches identify transcriptional mediators and epigenetic responses to Afghan desert particulate matter in small airway epithelial cells

3Citations
N/AReaders
Get full text

Genetic factors mediating long-range enhancer–promoter communication in mammalian development

1Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

White, S. M., Snyder, M. P., & Yi, C. (2021). Master lineage transcription factors anchor trans mega transcriptional complexes at highly accessible enhancer sites to promote long-range chromatin clustering and transcription of distal target genes. Nucleic Acids Research, 49(21), 12196–12210. https://doi.org/10.1093/nar/gkab1105

Readers over time

‘21‘22‘23‘24‘25036912

Readers' Seniority

Tooltip

PhD / Post grad / Masters / Doc 7

58%

Researcher 4

33%

Professor / Associate Prof. 1

8%

Readers' Discipline

Tooltip

Biochemistry, Genetics and Molecular Bi... 7

70%

Medicine and Dentistry 1

10%

Social Sciences 1

10%

Neuroscience 1

10%

Save time finding and organizing research with Mendeley

Sign up for free
0