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Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein ta...

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Autores principales: Holmqvist, Erik, Wright, Patrick R, Li, Lei, Bischler, Thorsten, Barquist, Lars, Reinhardt, Richard, Backofen, Rolf, Vogel, Jörg
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5207318/
https://www.ncbi.nlm.nih.gov/pubmed/27044921
http://dx.doi.org/10.15252/embj.201593360
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author Holmqvist, Erik
Wright, Patrick R
Li, Lei
Bischler, Thorsten
Barquist, Lars
Reinhardt, Richard
Backofen, Rolf
Vogel, Jörg
author_facet Holmqvist, Erik
Wright, Patrick R
Li, Lei
Bischler, Thorsten
Barquist, Lars
Reinhardt, Richard
Backofen, Rolf
Vogel, Jörg
author_sort Holmqvist, Erik
collection PubMed
description The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3′‐located Rho‐independent terminators as a universal motif involved in Hfq–RNA interactions. Additionally, Hfq preferentially binds 5′ to sRNA‐target sites in mRNAs, and 3′ to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA‐target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP‐seq approach will bring new insights into post‐transcriptional gene regulation by RNA‐binding proteins in diverse bacterial species.
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spelling pubmed-52073182017-01-04 Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo Holmqvist, Erik Wright, Patrick R Li, Lei Bischler, Thorsten Barquist, Lars Reinhardt, Richard Backofen, Rolf Vogel, Jörg EMBO J Resources The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3′‐located Rho‐independent terminators as a universal motif involved in Hfq–RNA interactions. Additionally, Hfq preferentially binds 5′ to sRNA‐target sites in mRNAs, and 3′ to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA‐target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP‐seq approach will bring new insights into post‐transcriptional gene regulation by RNA‐binding proteins in diverse bacterial species. John Wiley and Sons Inc. 2016-04-04 2016-05-02 /pmc/articles/PMC5207318/ /pubmed/27044921 http://dx.doi.org/10.15252/embj.201593360 Text en © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Resources
Holmqvist, Erik
Wright, Patrick R
Li, Lei
Bischler, Thorsten
Barquist, Lars
Reinhardt, Richard
Backofen, Rolf
Vogel, Jörg
Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
title Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
title_full Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
title_fullStr Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
title_full_unstemmed Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
title_short Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
title_sort global rna recognition patterns of post‐transcriptional regulators hfq and csra revealed by uv crosslinking in vivo
topic Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5207318/
https://www.ncbi.nlm.nih.gov/pubmed/27044921
http://dx.doi.org/10.15252/embj.201593360
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