Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression

Tim Y. Hou, W. Lee Kraus

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

To better understand the functions of non-coding enhancer RNAs (eRNAs), we annotated the estrogen-regulated eRNA transcriptome in estrogen receptor α (ERα)-positive breast cancer cells using PRO-cap and RNA sequencing. We then cloned a subset of the eRNAs identified, fused them to single guide RNAs, and targeted them to their ERα enhancers of origin using CRISPR/dCas9. Some of the eRNAs tested modulated the expression of cognate, but not heterologous, target genes after estrogen treatment by increasing ERα recruitment and stimulating p300-catalyzed H3K27 acetylation at the enhancer. We identified a ∼40 nucleotide functional eRNA regulatory motif (FERM) present in many eRNAs that was necessary and sufficient to modulate gene expression, but not the specificity of activation, after estrogen treatment. The FERM interacted with BCAS2, an RNA-binding protein amplified in breast cancers. The ectopic expression of a targeted eRNA controlling the expression of an oncogene resulted in increased cell proliferation, demonstrating the regulatory potential of eRNAs in breast cancer.

Original languageEnglish (US)
Article number110944
JournalCell Reports
Volume39
Issue number11
DOIs
StatePublished - Jun 14 2022

Keywords

  • Breast cancer
  • coregulator
  • CP: Molecular biology
  • enhancer
  • enhancer RNA (eRNA)
  • estrogen receptor alpha (ERα)
  • H3K27 acetylation
  • noncoding RNA
  • p300/CBP
  • pre-mRNA-splicing factor (SPF27/BCAS2)
  • transcription

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Fingerprint

Dive into the research topics of 'Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression'. Together they form a unique fingerprint.

Cite this