GENOME-WIDE IDENTIFICATION OF RNA SENSORS IN PROKARYOTES AND EUKARYOTES

Abstract

RNA's ability to fold into complex secondary and tertiary structures underlies its suitability as cellular sensors that detect and respond to metabolite changes in the environment. Here, we introduce a high-throughput strategy named PARCEL that directly and experimentally identifies RNA sensors genome-wide. Applying PARCEL to a collection of prokaryotic and eukaryotic organisms revealed 58 novel RNA sensors. The newly identified RNA sensors exhibit significant sequence and structure conservation, but an unexpected prevalence outside of non-coding regions and with new structural motifs. We identified a precursor tmRNA that acts as an RNA sensor for FMN to facilitate tmRNA maturation as well as an entirely new class of eukaryotic RNA sensors that recognize vitamin B2 (FMN) to control gene expression. This collection of RNA sensors expands our understanding of RNA function in the cell and suggests that RNA based sensing and gene regulation is much more widespread than previously appreciated.