Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity

Abstract

Graphical AbstractHighlights d eRNA-producing centers (EPCs) can be readily annotated from DHS and GRO-seq data d EPCs that serve as lncRNA promoters are associated with more active enhancers d lncRNA splicing is associated with higher enhancer activity d The ability to drive lncRNA production is a conserved feature of some enhancers Authors Noa Gil, Igor Ulitsky Correspondence igor.ulitsky@weizmann.ac.il In BriefTwo structurally distinct species of noncoding RNAs, eRNAs and lncRNAs, are produced from enhancers, but functional implications are unclear. We find that lncRNA-producing enhancers are more active and that this heightened activity is driven by conserved, directional splicing signals, indicating a causal role of lncRNA processing in enhancer activity. SUMMARYActive enhancers in mammals produce enhancer RNAs (eRNAs) that are bidirectionally transcribed, unspliced, and unstable. Enhancer regions are also enriched with long noncoding RNA (lncRNA) transcripts, which are typically spliced and substantially more stable. In order to explore the relationship between these two classes of RNAs, we analyzed DNase hypersensitive sites with evidence of bidirectional transcription, which we termed eRNA-producing centers (EPCs). EPCs found very close to transcription start sites of lncRNAs exhibit attributes of both enhancers and promoters, including distinctive DNA motifs and a characteristic chromatin landscape. These EPCs are associated with higher enhancer activity, driven at least in part by the presence of conserved, directional splicing signals that promote lncRNA production, pointing at a causal role of lncRNA processing in enhancer activity. Together, our results suggest that the conserved ability of some enhancers to produce lncRNAs augments their activity in a manner likely mediated through lncRNA maturation.

Splicing of enhancer-associated lincRNAs contributes to enhancer activity

“…The association between elincRNA splicing and cognate enhancer activity is supported by their enrichment in enhancer epigenetic signatures; greater fold increase in putative cis-target expression; and the modulation of local chromosomal architecture. Our results in mouse are also consistent with recent work in human cells, which also supports that multi-exonic lincRNAs are often transcribed from highly active enhancers (Gil & Ulitsky, 2018). Given the paucity of evidence supporting a sequence-dependent mechanism for most elincRNAs and their poor exonic nucleotide conservation, unexpectedly, we found splicing of elincRNAs is efficient.…”

“…Removal of the splicing signals in another elincRNA, Haunt, by replacing its endogenous locus with its cDNA, could not rescue its cis-regulatory function (Yin et al, 2015). Recently, the genome-wide analysis of enhancer transcription across multiple human cells lines (Gil & Ulitsky, 2018) corroborates candidate loci analyses, supporting the association between elincRNA splicing and cognate enhancer activity.…”

Gene regulation by long non-coding RNAs and its biological functions

“…Some enhancer loci produce elncRNAs, the expression of which is related to that of their enhancer elements 103 – 106 . Notably, elncRNA splicing has been positively associated with the activity of their associated enhancers and correlated with the abundance of the neighbouring protein-coding genes 107 , 108 . Furthermore, elncRNAs can modulate chromatin structure and topology in cooperation with chromatin-regulating proteins 40 , 109 .…”

Predictive models of subcellular localization of long RNAs

“…Inefficient splicing may help place lncRNAs at different subnuclear compartments and poise them for specific activities. Conversely, splicing itself is reported to be important for the functions of at least some lncRNAs (Engreitz et al 2016;Gil and Ulitsky 2018;Tan et al 2018). Regulated splicing can further assist in "releasing" the RNA from one compartment to another, allowing precise timing of its functional activity.…”