Production of spliced long noncoding RNAs specifies regions with increased enhancer activity

Abstract

Active enhancers in mammals produce enhancer RNAs (eRNAs), that are bidirectionally transcribed, unspliced, and unstable noncoding RNAs. Enhancer regions are also enriched with long noncoding RNA (lncRNA) genes, which are typically spliced and are longer and substantially more stable than eRNAs. In order to explore the relationship between these two classes of RNAs and the implications of lncRNA transcription on enhancer functionality, we analyzed DNAse hypersensitive sites with evidence of bidirectional transcription, which we termed eRNA producing centers (EPCs). A subset of EPCs, which are found very close to the transcription start site of lncRNA genes, exhibit attributes of both enhancers and promoters, including distinctive DNA motifs and a characteristic landscape of bound proteins. These EPCs are associated with a subset of relatively highly active enhancers. This stronger enhancer activity is driven, at least in part, by the presence of evolutionary conserved, directional splicing signals that promote lncRNA production, pointing at a causal role of lncRNA processing in enhancer activity. Together, our results suggest a model whereby the ability of some enhancers to produce lncRNAs, which is conserved in evolution, enhances their activity in a manner likely mediated through maturation of the associated lncRNA.

Impact of 3-dimensional genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver

“…The highly female-biased gene A1bg is nearby many lncRNAs, however, we observed that a subset of interacting lncRNAs was consistently femalebiased across different studies, experiment types, and mouse strains ( Figure S5C,D) -suggestive they may play a functional role. Currently, enhancer-associated lncRNAs are defined as those transcribed from enhancers and show interesting properties such as increased enhancer activity, tissue-specificity, and association with expression of nearby protein coding genes [78,79]. Our 4C-seq results for the A1bg enhancer suggest that this model could be extended to enhancer-interacting lncRNAs as an approach to characterize or screen for candidate functional lncRNAs.…”

The regulatory landscape of early maize inflorescence development

“…Based on our knowledge of gene regulation in other systems, at least some of these distal accessible regions may mark enhancers of gene expression. Reports in both animal and plant systems have linked enhancers with transcription of long non-coding RNAs (lncRNAs), which have been shown to control distal gene expression in various ways [42][43][44]; e.g., aiding chromatin looping to modulate expression of adjacent or distant PCGs [45][46][47].…”

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

“…These studies revealed that enhancer transcription often precedes target promoter activation (De Santa et al 2010) and is positively correlated with target gene expression (De Santa et al 2010; Kim et al 2010; Arner et al 2015). The majority [>95% (Natoli and Andrau 2012; Gil and Ulitsky 2018; Tan et al 2020)] of enhancers is transcribed bidirectionally and gives rise to relatively short single exonic RNAs that are non-polyadenylated and unstable, generally referred to as eRNAs (Kim et al 2010). The remaining enhancers transcribe enhancer-associated long noncoding RNAs [elncRNAs (Marques et al 2013; Gil and Ulitsky 2018; Tan et al 2020)] predominantly in one direction (Natoli and Andrau 2012).…”

“…The majority [>95% (Natoli and Andrau 2012; Gil and Ulitsky 2018; Tan et al 2020)] of enhancers is transcribed bidirectionally and gives rise to relatively short single exonic RNAs that are non-polyadenylated and unstable, generally referred to as eRNAs (Kim et al 2010). The remaining enhancers transcribe enhancer-associated long noncoding RNAs [elncRNAs (Marques et al 2013; Gil and Ulitsky 2018; Tan et al 2020)] predominantly in one direction (Natoli and Andrau 2012). In contrast with eRNAs, elncRNAs are relatively stable, polyadenylated and can be spliced (Natoli and Andrau 2012).…”

“…In general, the absence of evolutionary constraint at eRNA/elncRNA exons (Marques et al 2013) argues that the function of most eRNAs/elncRNAs is unlikely to be encoded within their sequences. Yet a large fraction of elncRNAs is multi-exonic and recently, genome-wide analysis in multiple human cell lines (Gil and Ulitsky 2018) and mouse Embryonic Stem Cells (Tan et al 2020) revealed that their splicing positively impacts enhancer function. Enhancers that transcribe multi-exonic elncRNAs are enriched in enhancer-specific chromatin signatures, elevated binding of co-transcriptional regulators, increased local intra-chromosomal DNA contacts, and strengthened cis -regulation on target gene expression (Gil and Ulitsky 2018; Tan et al 2020).…”