Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

Abstract

Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures. Gene Ontology (GO) analysis revealed that eRNAs play key roles in human cell identity. Furthermore, we detected numerous known and novel functional RNA structures within eRNA regions. To better characterize the cis-regulatory effects of non-coding variation in these structural ncRNAs, we performed a comprehensive analysis of the genetic variants of structural ncRNAs in eRNA regions that are associated with inflammatory autoimmune diseases. Disease-associated variants of the structural ncRNAs were disproportionately enriched in immune-specific cell types. We also identified riboSNitches in lymphoid eRNAs and investigated the potential pathogenic mechanisms by which eRNAs might function in autoimmune diseases. Collectively, our findings offer valuable insights into the function of eRNAs and suggest that eRNAs might be effective diagnostic and therapeutic targets for human diseases.

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

“…In addition to primary structure heterogeneity, eRNAs demonstrate diverse secondary structures that model those seen in tRNAs, miRNAs, snRNAs, and lncRNAs (Cheng et al, 2015;Ren et al, 2017). Some eRNA molecules contain different domains with unique functions (Cajigas et al, 2018;Cichewicz et al, 2018;Tsai et al, 2018).…”

“…Nevertheless, emerging evidence implicates a role for eRNA itself in transcription regulation. On a genomic scale, eRNA transcription and induction of mRNA transcription at neighboring genes are correlated (Kim et al, 2010;Kaikkonen et al, 2013;Li et al, 2013;Andersson et al, 2014a;Arner et al, 2015;Cheng et al, 2015;Dorighi et al, 2017;Ren et al, 2017;Imamura et al, 2018). RNAP II is not only abundantly present at active enhancers, but appears to be critical to their function as ubiquitination and dismissal of RNAP II leads to enhancer decommission and downregulation of target genes (Tan et al, 2018).…”

“…Because of their biological roles in gene transcription, eRNAs serve as markers of active enhancers. eRNA transcription per se is able to identify in vivo enhancers that are "caught in the act" of regulating mRNA/gene expression and does so independently of the local chromatin state or transcription factor binding (Kim et al, 2010;Wang et al, 2011;Sanyal et al, 2012;Hah et al, 2013;Andersson et al, 2014a;Wu et al, 2014;Arner et al, 2015;Cheng et al, 2015;Ren et al, 2017;Imamura et al, 2018). For example, one study found that eRNA served as a better marker of active enhancers than H3K27ac (Tyssowski et al, 2018).…”

“…The ability to mark active enhancers in cells is an opportunity for unique insights, and several studies have begun to successfully utilize eRNA to mark active enhancer regions (Wang et al, 2011;Cauchy et al, 2016;Baillie et al, 2017;Denisenko et al, 2017;Henriques et al, 2018). eRNA expression profiles are highly tissue-specific (Koch et al, 2011;Djebali et al, 2012;Arner et al, 2015;Cheng et al, 2015;Ren et al, 2017) and can differentiate between different activation states of cells Denisenko et al, 2017). As there are many more enhancer regions than gene loci, utilizing eRNA may provide unique opportunities and advantages for diagnosing, prognosticating, treating, and understanding the pathogenesis of diseases that aren't afforded by current biomarkers.…”

“…Multiple genome-wide association studies have found that most disease associated mutations occur outside the coding genome, and that a majority of those occur in enhancers or their transcribed RNAs (Farh et al, 2014;Aune et al, 2017). Accordingly, eRNAs are beginning to be utilized to map specific disease states and show the ability to identify disease-specific variants in a broad range of diseases including autoimmunity, cancer, infectious disease, cardiac hypertrophy, recurrent pregnancy loss, psychiatric, and neurological disorders (Farh et al, 2014;Witte et al, 2015;Liang et al, 2016;Aune et al, 2017;Le Gras et al, 2017;Ren et al, 2017;Hauberg et al, 2018;Huang Z. et al, 2018;Imamura et al, 2018;Jiao et al, 2018;Gu et al, 2019;Kyzar et al, 2019;Mirtschink et al, 2019;Tan et al, 2019). The therapeutic potential of these studies was demonstrated when knockdown of the HERNA1 eRNA, which promotes pathological cardiac hypertrophy, protected mice from disease and reversed pathology in mice that had already developed the disease (Mirtschink et al, 2019).…”