The activity of human enhancers is modulated by the splicing of their associated lncRNAs

Abstract

1Pervasive enhancer transcription is at the origin of more than half of all long 2 noncoding RNAs in humans. Transcription of enhancer-associated long 3 noncoding RNAs (elncRNA) contribute to their cognate enhancer activity and 4 gene expression regulation in cis. Recently, splicing of elncRNAs was shown 5 to be associated with elevated enhancer activity. However, whether splicing of 6 elncRNA transcripts is a mere consequence of accessibility at highly active 7 enhancers or if elncRNA splicing directly impacts enhancer function, remains 8 unanswered. 9We analysed genetically driven changes in elncRNA expression, in humans, to 10 address this outstanding question. We showed that splicing related motifs 11 within multi-exonic elncRNAs evolved under selective constraints during human 12 evolution, suggesting the processing of these transcripts is unlikely to have 13 resulted from transcription across spurious splice sites. Using a genome-wide 14 and unbiased approach, we used nucleotide variants as independent genetic 15 factors to directly assess the causal relationship that underpin elncRNA splicing 16and their cognate enhancer activity. We found that the splicing of most 17 elncRNAs is associated with changes in chromatin signatures at cognate 18 enhancers and target mRNA expression. 19We conclude that efficient and conserved processing of enhancer-associated 20 elncRNAs contributes to enhancer activity. 21 22

Long non-coding RNAs: definitions, functions, challenges and recommendations

“…Also analogously to mRNAs produced from protein-coding genes, enhancers express long (non-coding) RNAs (confusingly also referred to as 'eRNAs' 298,306 ), and transcription is considered the best molecular indicator of enhancer activity in developmental processes 296,297,[306][307][308] and cancers 288 . Moreover, enhancer-lncRNA splicing has been shown to modulate enhancer activity 309,310 .…”

Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation

“…A common denominator of these RNAs is a relatively high expression in unstimulated conditions and efficient splicing, which has been linked with more efficient enhancer activity in broad regions flanking the spliced lncRNAs (Gil and Ulitsky 2018; Jennifer Y. Tan et al 2020; Jennifer Yihong Tan and Marques 2022). It is, therefore, possible that transcription of Silc1 and its splicing enables the proper positioning of the broad Sox11 locus in a nuclear and chromatin environment that facilitates a stronger response to stimulus, such as that which occurs when mice are exposed to NE.…”