Sartorelli_2020: Enhancer RNAs are an important regulatory layer of the epigenome

keywords

Enhancer RNA (eRNA)

Enhancer RNAs

Introduction

eRNAs

A recent addition to the expanding list of regulatory ncRNAs is the emerging class of enhancer RNAs (eRNAs), which are transcribed from enhancers in a tissue-specific manner.

Regulatory Non-coding RNAs that are transcribed from enhancers in a tissue specific manner

RNA-mediate gene regulation

Enhancer definition

Enhancers are classically defined as DNA sequences that regulate the gene expression networks underlying distinct cellular identities and cellular responses to environmental cues

Many different models for how enhancers function in gene control have been proposed since their initial discovery nearly four decades ago

Key study revealed that experimental induction of Chromatin Looping between the mouse β-globin (Hbb) Promoter and its associated enhancer region results in transcriptional activation of the Hbb gene

Additional analyses of the forced looping of the Hbb enhancer and promoter regions revealed that enhancer–promoter contacts affect transcription by supporting an increase in the transcriptional burst fraction (number of transcribing alleles), although the burst size (number of transcripts produced) was unaltered

Enhancers may also regulate target genes via transcripts produced from the enhancer regions themselves

However, an issue that remains to be resolved is whether eRNAs have direct roles in gene control, as current efforts to determine this face the challenge of uncoupling eRNA function from the act of enhancer transcription. Thus, it remains necessary to develop tools to experimentally manipulate and model the direct functions of eRNAs

Enhancers as functional noncoding RNA transcription units

Because eRNAs are not readily detectable in steady-state RNA-sequencing data, their annotation depends on sequencing nascent RNA using approaches that include GRO-seq, precision run-on nuclear sequencing (PRO-seq) and Cap Analysis Gene Expression (CAGE) These nascent transcription assays have been instrumental in uncovering a wide array of ncRNAs, including long noncoding RNAs, enhancer RNAs, promoter upstream transcripts and upstream antisense RNAs. Indeed, global annotation analyses have revealed that eRNA transcripts account for a large proportion of initiation events in the transcriptome, with approximately 40,000–65,000 eRNAs expressed in human cells. The annotation of such transcripts in Drosophila melanogaster and Caenorhabditis elegans reinforces the finding that eRNAs are a common feature of active enhancers in metazoans

eRNAs are produced from active enhancers that share several features:

  1. An open chromatin state, reflected by the presence of DNase hypersensitive sites (DHSs)

  2. Binding of transcription factors and cofactors, including the Histone Acetyltransferase p300 and cAMP response element–binding protein (CBP)

  3. the co-occurrence of histone H3 lysine 4 monomethylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac)

Regulation of enhancer transcription

Studies in Drosophila have also revealed that bidirectionally transcribed enhancers behave as weak promoters and, conversely, that bidirectionally transcribed promoters can function as strong enhancers. These findings blur the classical definitions of promoters and enhancers and raise the possibility that noncoding transcripts generated at both regulatory regions may be functional

There are discernible differences between the transcriptional elongation phases of eRNA and mRNA transcript production

Tyr1P

Classification of noncoding enhancer RNAs