RNA secondary structome of different cell lines
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we resolved the RNA secondary structure of human (HEK293, HeLa, K562, HepG2, H9) and mouse (mES) cells based on optimized in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). we describe a deep discriminative neural network (PrismNet) that integrates big data of RBP binding and RNA secondary structure from matched living cells and accurately models the RNA sequence and structural preferences of protein-RNA interactions in vivo, enabling precise prediction of the perturbation effects of genetic variants. Libraries of 7 cell lines (human: HEK293, HeLa, K562, HepG2, H9 and mouse : mES) were constructed as the optimized icSHAPE protocol. The RNA structure in vivo was calculated based on DMSO samples (D), in vivo NAI-N3 treatment samples (N) by the new protocol icSHAPE-pipe.
