Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors [SHAPE-MaP]

Many lncRNAs have been discovered using transcriptomic data, however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs. SHAPE-MaP on RNA from C2C12 cells overexpressing MUNC variants for a total 16 samples (8 DMSO, 85NIA): Cell-free SHAPE of 2 MUNC spliced replicates, MUNC genomic, CH1 deletion, and CH4 deletion; In-cell SHAPE of 2 replicates of MUNC spliced and 1 replicate of MUNC genomic