![]() ![]() Small, non-coding RNAs (sRNAs) that associate with the RNA chaperone Hfq constitute the largest class of post-transcriptional regulators in Gram-negative bacteria ( De Lay et al., 2013, Storz et al., 2011, Vogel and Luisi, 2011, Wagner and Romby, 2015). Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators. In vivo, the processing is required for target regulation. ![]() Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. 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 3′ fragments from various precursor RNAs. ![]() 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. 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. Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. ![]()
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