MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation

Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. We demonstrate the critical role of MyoD in activating eRNAs production. Results from in depth dissection of two eRNAs transcribed from super enhancers (seRNA-1 and -2) suggest that seRNAs can promote myogenic differentiation in vitro and in vivo; the induction of the seRNAs is in coordination with the activation of the neighboring genes and seRNA loss largely impairs their expression. Mechanistically, we elucidate these seRNAs specifically bind to heterogeneous nuclear ribonucleoprotein L (hnRNPL) and modulate hnRNPL binding to the target promoter. A CAAA tract on the seRNA was identified to be essential in mediating the interaction between seRNA-1 and hnRNPL. Disruption of seRNA-hnRNPL interaction attenuates Pol II and H3K36me3 deposition at the target genes, in coincidence with the reduction of their expression. Furthermore, analyses of hnRNPL binding transcriptome-wide reveals its association with eRNAs is a general phenomenon in multiple cells. Collectively, we propose that eRNA-hnRNPL interaction contributes to target mRNA activation. 2 RNA-seq, 1 hnRNPL CLIP-seq, 8 GRO-seq experiments performed.