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Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation

Hfq is a global regulator of gene expression in bacteria undergoing adaptation to changing environmental conditions. Its major function is to promote RNA-RNA interactions between regulatory small RNAs (sRNAs) and their target mRNAs. Previously, we demonstrated that Hfq binds many antisense RNAs (asR...

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Autores principales: Bilusic, Ivana, Popitsch, Niko, Rescheneder, Philipp, Schroeder, Renée, Lybecker, Meghan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Landes Bioscience 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152368/
https://www.ncbi.nlm.nih.gov/pubmed/24922322
http://dx.doi.org/10.4161/rna.29299
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author Bilusic, Ivana
Popitsch, Niko
Rescheneder, Philipp
Schroeder, Renée
Lybecker, Meghan
author_facet Bilusic, Ivana
Popitsch, Niko
Rescheneder, Philipp
Schroeder, Renée
Lybecker, Meghan
author_sort Bilusic, Ivana
collection PubMed
description Hfq is a global regulator of gene expression in bacteria undergoing adaptation to changing environmental conditions. Its major function is to promote RNA-RNA interactions between regulatory small RNAs (sRNAs) and their target mRNAs. Previously, we demonstrated that Hfq binds many antisense RNAs (asRNAs) in vitro and hypothesized that Hfq may play a role in regulating gene expression via asRNAs. To investigate the E. coli Hfq-binding transcriptome in more detail, we co-immunoprecipitated and deep-sequenced RNAs bound to Hfq in vivo. We detected many new Hfq-binding sRNAs and observed that almost 300 mRNAs bind to Hfq. Among these, several are known to be sRNA targets. We identified 25 novel RNAs, which are transcribed from within protein coding regions and named them intragenic RNAs (intraRNAs). Furthermore, 67 asRNAs were co-immunoprecipitated with Hfq, demonstrating that Hfq binds antisense transcripts in vivo. Northern blot analyses confirmed the deep sequencing results and demonstrated that many of the novel Hfq-binding RNAs identified are regulated by Hfq.
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spelling pubmed-41523682015-06-12 Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation Bilusic, Ivana Popitsch, Niko Rescheneder, Philipp Schroeder, Renée Lybecker, Meghan RNA Biol Research Paper Hfq is a global regulator of gene expression in bacteria undergoing adaptation to changing environmental conditions. Its major function is to promote RNA-RNA interactions between regulatory small RNAs (sRNAs) and their target mRNAs. Previously, we demonstrated that Hfq binds many antisense RNAs (asRNAs) in vitro and hypothesized that Hfq may play a role in regulating gene expression via asRNAs. To investigate the E. coli Hfq-binding transcriptome in more detail, we co-immunoprecipitated and deep-sequenced RNAs bound to Hfq in vivo. We detected many new Hfq-binding sRNAs and observed that almost 300 mRNAs bind to Hfq. Among these, several are known to be sRNA targets. We identified 25 novel RNAs, which are transcribed from within protein coding regions and named them intragenic RNAs (intraRNAs). Furthermore, 67 asRNAs were co-immunoprecipitated with Hfq, demonstrating that Hfq binds antisense transcripts in vivo. Northern blot analyses confirmed the deep sequencing results and demonstrated that many of the novel Hfq-binding RNAs identified are regulated by Hfq. Landes Bioscience 2014-05-01 2014-06-12 /pmc/articles/PMC4152368/ /pubmed/24922322 http://dx.doi.org/10.4161/rna.29299 Text en Copyright © 2014 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
spellingShingle Research Paper
Bilusic, Ivana
Popitsch, Niko
Rescheneder, Philipp
Schroeder, Renée
Lybecker, Meghan
Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
title Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
title_full Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
title_fullStr Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
title_full_unstemmed Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
title_short Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation
title_sort revisiting the coding potential of the e. coli genome through hfq co-immunoprecipitation
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152368/
https://www.ncbi.nlm.nih.gov/pubmed/24922322
http://dx.doi.org/10.4161/rna.29299
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