The transcription factor ERG regulates super-enhancers associated with an endothelial-specific gene expression program
File(s)
Published version
Supplementary information
Author(s)
Type
Journal Article
Abstract
Rationale:
The ETS (E-26 transformation-specific) transcription factor ERG (ETS-related gene) is essential for endothelial homeostasis, driving expression of lineage genes and repressing proinflammatory genes. Loss of ERG expression is associated with diseases including atherosclerosis. ERG’s homeostatic function is lineage-specific, because aberrant ERG expression in cancer is oncogenic. The molecular basis for ERG lineage-specific activity is unknown. Transcriptional regulation of lineage specificity is linked to enhancer clusters (super-enhancers).
Objective:
To investigate whether ERG regulates endothelial-specific gene expression via super-enhancers.
Methods and Results:
Chromatin immunoprecipitation with high-throughput sequencing in human umbilical vein endothelial cells showed that ERG binds 93% of super-enhancers ranked according to H3K27ac, a mark of active chromatin. These were associated with endothelial genes such as DLL4 (Delta-like protein 4), CLDN5 (claudin-5), VWF (von Willebrand factor), and CDH5 (VE-cadherin). Comparison between human umbilical vein endothelial cell and prostate cancer TMPRSS2 (transmembrane protease, serine-2):ERG fusion-positive human prostate epithelial cancer cell line (VCaP) cells revealed distinctive lineage-specific transcriptome and super-enhancer profiles. At a subset of endothelial super-enhancers (including DLL4 and CLDN5), loss of ERG results in significant reduction in gene expression which correlates with decreased enrichment of H3K27ac and MED (Mediator complex subunit)-1, and reduced recruitment of acetyltransferase p300. At these super-enhancers, co-occupancy of GATA2 (GATA-binding protein 2) and AP-1 (activator protein 1) is significantly lower compared with super-enhancers that remained constant following ERG inhibition. These data suggest distinct mechanisms of super-enhancer regulation in endothelial cells and highlight the unique role of ERG in controlling a core subset of super-enhancers. Most disease-associated single nucleotide polymorphisms from genome-wide association studies lie within noncoding regions and perturb transcription factor recognition sequences in relevant cell types. Analysis of genome-wide association studies data shows significant enrichment of risk variants for cardiovascular disease and other diseases, at ERG endothelial enhancers and super-enhancers.
Conclusions:
The transcription factor ERG promotes endothelial homeostasis via regulation of lineage-specific enhancers and super-enhancers. Enrichment of cardiovascular disease-associated single nucleotide polymorphisms at ERG super-enhancers suggests that ERG-dependent transcription modulates disease risk.
The ETS (E-26 transformation-specific) transcription factor ERG (ETS-related gene) is essential for endothelial homeostasis, driving expression of lineage genes and repressing proinflammatory genes. Loss of ERG expression is associated with diseases including atherosclerosis. ERG’s homeostatic function is lineage-specific, because aberrant ERG expression in cancer is oncogenic. The molecular basis for ERG lineage-specific activity is unknown. Transcriptional regulation of lineage specificity is linked to enhancer clusters (super-enhancers).
Objective:
To investigate whether ERG regulates endothelial-specific gene expression via super-enhancers.
Methods and Results:
Chromatin immunoprecipitation with high-throughput sequencing in human umbilical vein endothelial cells showed that ERG binds 93% of super-enhancers ranked according to H3K27ac, a mark of active chromatin. These were associated with endothelial genes such as DLL4 (Delta-like protein 4), CLDN5 (claudin-5), VWF (von Willebrand factor), and CDH5 (VE-cadherin). Comparison between human umbilical vein endothelial cell and prostate cancer TMPRSS2 (transmembrane protease, serine-2):ERG fusion-positive human prostate epithelial cancer cell line (VCaP) cells revealed distinctive lineage-specific transcriptome and super-enhancer profiles. At a subset of endothelial super-enhancers (including DLL4 and CLDN5), loss of ERG results in significant reduction in gene expression which correlates with decreased enrichment of H3K27ac and MED (Mediator complex subunit)-1, and reduced recruitment of acetyltransferase p300. At these super-enhancers, co-occupancy of GATA2 (GATA-binding protein 2) and AP-1 (activator protein 1) is significantly lower compared with super-enhancers that remained constant following ERG inhibition. These data suggest distinct mechanisms of super-enhancer regulation in endothelial cells and highlight the unique role of ERG in controlling a core subset of super-enhancers. Most disease-associated single nucleotide polymorphisms from genome-wide association studies lie within noncoding regions and perturb transcription factor recognition sequences in relevant cell types. Analysis of genome-wide association studies data shows significant enrichment of risk variants for cardiovascular disease and other diseases, at ERG endothelial enhancers and super-enhancers.
Conclusions:
The transcription factor ERG promotes endothelial homeostasis via regulation of lineage-specific enhancers and super-enhancers. Enrichment of cardiovascular disease-associated single nucleotide polymorphisms at ERG super-enhancers suggests that ERG-dependent transcription modulates disease risk.
Date Issued
2019-04-26
Date Acceptance
2019-03-18
Citation
Circulation Research, 2019, 124 (9), pp.1337-1349
ISSN
0009-7330
Publisher
American Heart Association
Start Page
1337
End Page
1349
Journal / Book Title
Circulation Research
Volume
124
Issue
9
Copyright Statement
© 2019 The Authors. Circulation Research is published on behalf of the American Heart Association, Inc., by Wolters Kluwer Health, Inc. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution, and reproduction in any medium, provided that the original work is properly cited.
Sponsor
British Heart Foundation
British Heart Foundation
British Heart Foundation
British Heart Foundation
British Heart Foundation
Identifier
https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.118.313788
Grant Number
RG/11/17/29256
RG/17/4/32662
PG/17/33/32990
FS/13/12/30037
SCRF03
Subjects
Science & Technology
Life Sciences & Biomedicine
Cardiac & Cardiovascular Systems
Hematology
Peripheral Vascular Disease
Cardiovascular System & Cardiology
chromatin
endothelial cells
endothelium
homeostasis
transcription factors
GENOME-WIDE ASSOCIATION
ANDROGEN RECEPTOR
CELL IDENTITY
ANGIOGENESIS
INFLAMMATION
INHIBITION
ACTIVATION
CHROMATIN
NETWORK
chromatin
endothelial cells
endothelium
homeostasis
transcription factors
Cell Line, Tumor
Cells, Cultured
Claudin-5
Enhancer Elements, Genetic
GATA2 Transcription Factor
Gene Expression Profiling
Gene Expression Regulation
Human Umbilical Vein Endothelial Cells
Humans
Intracellular Signaling Peptides and Proteins
Male
Membrane Proteins
Prostatic Neoplasms
Serine Endopeptidases
Transcription Factor AP-1
Transcriptional Regulator ERG
Cells, Cultured
Cell Line, Tumor
Humans
Prostatic Neoplasms
Serine Endopeptidases
Intracellular Signaling Peptides and Proteins
Membrane Proteins
Transcription Factor AP-1
Gene Expression Profiling
Gene Expression Regulation
Male
GATA2 Transcription Factor
Enhancer Elements, Genetic
Human Umbilical Vein Endothelial Cells
Claudin-5
Transcriptional Regulator ERG
Cardiovascular System & Hematology
1102 Cardiorespiratory Medicine and Haematology
1103 Clinical Sciences
Publication Status
Published
Date Publish Online
2019-03-20