eRNAs

Enhancer RNAs (eRNAs) are a class of non-coding RNA transcripts that originate from enhancer regions in the genome. They are typically produced by RNA polymerase II at active enhancers and are often transcribed in a bidirectional fashion from loci marked by enhancer-associated chromatin signatures such as H3K4me1 and H3K27ac. eRNAs are usually short, unstable transcripts that are not routinely polyadenylated, and they tend to have short half-lives compared with messenger RNAs. Their expression is highly tissue- and stimulus-specific and generally correlates with the activity of the nearby enhancer and the transcriptional output of their target genes.

The functional significance of eRNAs remains a topic of research and debate. In some contexts, the presence of eRNA transcription correlates with higher enhancer activity and with elevated expression of nearby genes; perturbations that reduce eRNA production can sometimes decrease target gene expression or affect enhancer-promoter looping. However, other studies suggest that eRNA transcription can be a byproduct of an active enhancer rather than a required mechanism, and not all enhancers producing transcripts show a measurable regulatory effect on gene expression.

eRNAs are typically detected using methods that capture transcription or nascent RNA, such as global run-on sequencing (GRO-seq) and precision run-on sequencing (PRO-seq), or RNA sequencing approaches that enrich for nascent transcripts. They are generally shorter than 2 kilobases and are rapidly degraded, contributing to challenges in detection by standard RNA-seq. eRNA biology is an active field, with ongoing work to determine the extent to which individual eRNAs contribute causally to gene regulation.