Massively Parallel Dissection of RNA in RNA-protein interactions in vivo Journal Article uri icon



  • ABSTRACTMany of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to molecular biology. Here, we present MPRNA-immunoprecipitation (MPRNA-IP), an adaptation of the previously developed massively parallel RNA assay (MPRNA), and a new avenue for in vivo high-throughput dissection of RNA-protein interactions. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, we are able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest including NORAD, MS2, and human telomerase RNA, and we describe statistical models for identifying RNA domains and parsing the structural contributions of RNA in these interactions. By blending modern and classical approaches, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions.

publication date

  • June 15, 2022

has restriction

  • green

Date in CU Experts

  • June 21, 2022 12:14 PM

Full Author List

  • Hass EP; Lee YH; Campodonico W; Lee YK; Lasda E; Shah JS; Rinn JL; Hwang T

author count

  • 8

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