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Chao, Yanjie; Li, Lei; Girodat, Dylan; Förstner, Konrad U.; Said, Nelly; Corcoran, Colin; Smiga, Michal; Papenfort, Kai; Reinhardt, Richard; Wieden, Hans-Joachim; Luisi, Ben F.; Vogel, Jörg (2017): In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. In: Molecular Cell, Vol. 65, No. 1: pp. 39-51
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Abstract

Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 30 fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators.