Rationale: The ETS transcription factor (TF) ERG is essential for endothelial homeostasis, driving
expression of lineage genes and repressing pro-inflammatory genes. Loss of ERG expression is associated
with diseases including atherosclerosis. ERG’s homeostatic function is lineage-specific, since 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 (ChIP-seq) in
human umbilical vein endothelial cells (HUVEC) 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, CLDN5, VWF and CDH5. Comparison between HUVEC and prostate cancer TMPRSS2:ERG
fusion-positive 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 Mediator subunit
MED1, and reduced recruitment of acetyltransferase p300. At these super-enhancers, co-occupancy of
GATA2 and AP-1 is significantly lower compared to super-enhancers that remained constant following
ERG inhibition. These data suggest distinct mechanisms of super-enhancer regulation in EC and highlight
the unique role of ERG in controlling a core subset of super-enhancers. Most disease-associated single
nucleotide polymorphisms (SNPs) from genome-wide association studies (GWAS) lie within noncoding
regions and perturb TF recognition sequences in relevant cell types. Analysis of GWAS data shows
significant enrichment of risk variants for CVD and other diseases, at ERG endothelial enhancers and superenhancers.
Conclusions: The TF ERG promotes endothelial homeostasis via regulation of lineage-specific enhancers
and super-enhancers. Enrichment of CVD-associated SNPs at ERG super-enhancers suggests that ERGdependent transcription modulates disease risk.This work was funded by grants from the British Heart Foundation (RG/11/17/29256; RG/17/4/32662;
FS/15/65/32036; PG/17/33/32990) and Cancer Research U