Transcriptome-wide RNA-protein interaction predictions

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.

Researchers at the University of California, Irvine extend these studies with the first transcriptome-wide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, the researchers 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, this 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. The researchers 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.

Schematic for icSHAPE and icLASER

Schematic for icSHAPE and icLASER. (A) Chemical protocol for icSHAPE (10) and icLASER. (B) Protocol for library preparation for icSHAPE and icLASER, which could be integrated in the same protocol method for RNA structure probing, transcriptome-wide. (C) Chemical structure of dibenzylcyclooctyne biotin (DBCO biotin) used for copper-free ‘click’ reaction with azido-modified structure probes. (D) Chemical structure of the final product between azido-modified structure probes and DBCO biotin.

(A) Chemical protocol for icSHAPE and icLASER. (B) Protocol for library preparation for icSHAPE and icLASER, which could be integrated in the same protocol method for RNA structure probing, transcriptome-wide. (C) Chemical structure of dibenzylcyclooctyne biotin (DBCO biotin) used for copper-free ‘click’ reaction with azido-modified structure probes. (D) Chemical structure of the final product between azido-modified structure probes and DBCO biotin.

Chan D, Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A, Spitale RC. (2021) Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Res [Epub ahead of print]. [article]

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