RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

We have ablated the cellular RNA degradation machinery in differentiated B cells and pluripotent embryonic stem cells (ESCs) by conditional mutagenesis of core (Exosc3) and nuclear RNase (Exosc10) components of RNA exosome and identified a vast number of long non-coding RNAs (lncRNAs) and enhancer RNAs (eRNAs) with emergent functionality. Unexpectedly, eRNA-expressing regions accumulate R-loop structures upon RNA exosome ablation, thus demonstrating the role of RNA exosome in resolving deleterious DNA/RNA hybrids arising from active enhancers. We have uncovered a distal divergent eRNA-expressing element (lncRNA-CSR) engaged in long-range DNA interactions and regulating IgH 3′ regulatory region super-enhancer function. CRISPR-Cas9-mediated ablation of lncRNA-CSR transcription decreases its chromosomal looping-mediated association with the IgH 3′ regulatory region super-enhancer and leads to decreased class switch recombination efficiency. We propose that the RNA exosome protects divergently transcribed lncRNA expressing enhancers by resolving deleterious transcription-coupled secondary DNA structures, while also regulating long-range super-enhancer chromosomal interactions important for cellular function. [Display omitted] •Identification of new lncRNAs and eRNAs from RNA exosome mutant transcriptomes•Transcribed enhancer sequences are protected from genomic instability by RNA exosome•Antisense RNAs substrates of the RNA exosome regulate super-enhancer activity•eRNA-expressing element (lncRNA-CSR) promotes recombination in the IgH locus The RNA exosome regulates the expression of non-coding RNAs originating from enhancer regions, helping to coordinate their function with the activity of neighboring super-enhancers.