Transcriptome-Wide Combinatorial RNA Structure Probing in Living Cells with icSHAPE and icLASER

We design and test a novel di-azido LASER reagent capable enrichment through attachment of biotin with strain-promoted azide alkyne cycloaddition (SPAAC). We term this approach in vivo click LASER or icLASER. Aligned with the goal of extending transcriptome-wide measurements of RNA structure and to develop an approach that takes advantage of combinatorial RNA structure probing,we then use this novel bi-functional probe to interrogate LASER reactivity transcriptome-wide, revealing the first solvent accessibility transcriptome map. We also directly compare icSHAPE (hydroxyl acylation; flexibility) and icLASER (solvent accessibility) to demonstrate the power of utilizing them together to predict RNA-protein interactions and RNA polyadenylation.Our results demonstrate that combinatorial RNA structure probing can be employed to compliment orthogonal methods to better understand RNA structure and processing in cells transcriptome-wide. Overall design: Fourteen total samples, consisting of three biological replicates each of: in vivo icSHAPE-treated, DMSO icSHAPE control, and two biological replicates each of: in vitro icSHAPE-treated, in vivo icLASER-treated, in vitro icLASER-treated, no-UV icLASER control