PT  - JOURNAL ARTICLE
AU  - Dalen Chan
AU  - Chao Feng
AU  - Whitney England
AU  - Dana Wyman
AU  - Ryan A. Flynn
AU  - Xiuye Wang
AU  - Yongsheng Shi
AU  - Ali Mortazavi
AU  - Robert C. Spitale
TI  - Transcriptome-Wide Combinatorial RNA Structure Probing in Living Cells
AID  - 10.1101/2020.03.24.006866
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.03.24.006866
4099  - http://biorxiv.org/content/early/2020/03/27/2020.03.24.006866.short
4100  - http://biorxiv.org/content/early/2020/03/27/2020.03.24.006866.full
AB  - RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptomewide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of designing novel chemical approaches to studying RNA biology. Further, our study exemplifies merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.