Enhancer RNAs: Insights Into Their Biological Role

Abstract

Enhancers play a central role in the transcriptional regulation of metazoans. Almost a decade ago, the discovery of their pervasive transcription into noncoding RNAs, termed enhancer RNAs (eRNAs), opened a whole new field of study. The presence of eRNAs correlates with enhancer activity; however, whether they act as functional molecules remains controversial. Here we review direct experimental evidence supporting a functional role of eRNAs in transcription and provide a general pipeline that could help in the design of experimental approaches to investigate the function of eRNAs. We propose that induction of transcriptional activity at enhancers promotes an increase in its activity by an RNA-mediated titration of regulatory proteins that can impact different processes like chromatin accessibility or chromatin looping. In a few cases, transcripts originating from enhancers have acquired specific molecular functions to regulate gene expression. We speculate that these transcripts are either nonannotated long noncoding RNAs (lncRNAs) or are evolving toward functional lncRNAs. Further work will be needed to comprehend better the biological activity of these transcripts.

Keywords: chromatin; chromatin loop; eRNAs; enhancer; gene expression; lncRNAs.

Figure 1.

Enhancer RNAs (eRNAs) can influence catalytic activity of chromatin modifier proteins or act as traps for transcription factors. Left, eRNAs can directly interact with CBP, a histone acetyltransferase, and stimulate its enzymatic activity which results in a eRNA concentration dependent increase of H3K27ac as well acetylation in other amino acid residues of histones. Right, eRNAs at enhancers can trap transcription factors, like YY1, which results in an increase of signal for YY1 as evaluated by ChIP. This could mean that association with eRNAs increases residency time of TFs. CBP indicates CREB binding protein; TF, transcription factors.

Figure 2.

eRNAs can stabilize chromatin long-range interactions between transcribing enhancers and target promoters. The NRIP1 promoter is in close proximity with an enhancer located ~250 kb upstream. Upon stimulation with estradiol, the transcription of both the enhancer and NRIP1 is induced. This transcriptional effect is accompanied by increased deposition of the cohesin subunits Rad21 and SMC3 at the enhancer, as well as an increased frequency of interaction between the enhancer and the NRIP1 promoter gene. This local reorganization is also accompanied by the gain of a novel interaction with TFF1, located 27 Mb away from NRIP1 gene that is also transcriptionally induced during estradiol treatment. Depletion of NRIP1-associated eRNAs results in loss of NRIP1 transcription, decreased deposition of cohesin subunits at the enhancer, and importantly, a decreased frequency of long-range interactions between the enhancer and the NRIP1 promoter gene as evaluated by 3C and the loss of the 27 Mb interaction as evaluated by fluorescence in situ hybridization. Of note, eRNAs can directly interact with cohesin subunits. eRNA indicates enhancer RNAs; KD, knockdown; ER, Estrogen Receptor.

Figure 3.

Enhancer RNAs (eRNAs) can promote exit of RNA Pol II pausing at promoters by mimicking nascent transcripts and interacting with NELF. The ARC locus is in physical proximity with an enhancer element throughout chromatin looping. Upon neuron stimulation, the transcription of both the enhancer and ARC gene is induced. Interestingly, transcription of one of the enhancer strands is more abundant. This eRNA can directly interact with NELF acting as a decoy for that protein. This results in loss of NELF at ARC promoter and the release of the paused RNA Pol II which engages in productive elongation. NELF indicates negative elongation factor; RNA Pol II, RNA polymerase II.