DMS-MaPseq of RORC reporters and endogeneous RORC locus [reporter cell lines]

RNA structural switches are key regulators of gene expression in bacteria, yet their characterization in Metazoa remains limited. Here we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3'UTR of the RORC transcript. In vivo DMS-MaPseq, coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated mRNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally-driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape. Overall design: To understand the dynamics of RORC RNA switch under differrent contexts, we established 5 RORC reporter cell lines (ZR-75-1 (breast), MCF-7 (breast), HepG2 (liver), LNCaP (prostate), LS174T (colon)) and performed targeted DMS-MaPseq of the RNA switch locus.