Summary
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 3′ 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.
%0 Journal Article
%1 chao_vivo_2017
%A Chao, Yanjie
%A Li, Lei
%A Girodat, Dylan
%A Förstner, Konrad U.
%A Said, Nelly
%A Corcoran, Colin
%A Śmiga, Michał
%A Papenfort, Kai
%A Reinhardt, Richard
%A Wieden, Hans-Joachim
%A Luisi, Ben F.
%A Vogel, Jörg
%D 2017
%J Molecular Cell
%K 3′_UTR ArcZ Hfq RNA_degradome RNase_E RprA TIER-seq non-coding_RNA sRNA_maturation uridine_ruler
%N 1
%P 39--51
%R 10.1016/j.molcel.2016.11.002
%T In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways
%U http://www.sciencedirect.com/science/article/pii/S1097276516307109
%V 65
%X Summary
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 3′ 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.
@article{chao_vivo_2017,
abstract = {Summary
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 3′ 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.},
added-at = {2019-10-23T15:12:39.000+0200},
author = {Chao, Yanjie and Li, Lei and Girodat, Dylan and Förstner, Konrad U. and Said, Nelly and Corcoran, Colin and Śmiga, Michał and Papenfort, Kai and Reinhardt, Richard and Wieden, Hans-Joachim and Luisi, Ben F. and Vogel, Jörg},
biburl = {https://www.bibsonomy.org/bibtex/2d68ad3fc88864ca3f0312cee0ed885cf/cusysmed},
doi = {10.1016/j.molcel.2016.11.002},
interhash = {e5ebe41cc3fa65eab558beb1e0107acc},
intrahash = {d68ad3fc88864ca3f0312cee0ed885cf},
issn = {1097-2765},
journal = {Molecular Cell},
keywords = {3′_UTR ArcZ Hfq RNA_degradome RNase_E RprA TIER-seq non-coding_RNA sRNA_maturation uridine_ruler},
month = jan,
number = 1,
pages = {39--51},
timestamp = {2019-10-23T15:12:39.000+0200},
title = {In {Vivo} {Cleavage} {Map} {Illuminates} the {Central} {Role} of {RNase} {E} in {Coding} and {Non}-coding {RNA} {Pathways}},
url = {http://www.sciencedirect.com/science/article/pii/S1097276516307109},
urldate = {2018-06-22},
volume = 65,
year = 2017
}