Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
- University of Edinburgh, United Kingdom
- CNR, Italy
- University of New South Wales, Australia
- CNR Unit, Italy
Abstract
By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3'UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.
Data availability
The next generation sequencing data have been deposited on the NCBI Gene Expression Omnibus (GEO) with accession number GSE123050. The python pyCRAC (Webb et al., 2014), kinetic-CRAC and GenomeBrowser software packages used for analysing the data are available from https://bitbucket.org/sgrann (pyCRAC up to version 1.4.3), https://git.ecdf.ed.ac.uk/sgrannem/ and pypi (https://pypi.org/user/g_ronimo/). The hyb pipeline for identifying chimeric reads is available from https://github.com/gkudla/hyb. The scripts for statistical analysis of hyb data is available from https://bitbucket.org/jaitree/hyb_stats/. The FLASH algorithm for merging paired reads is available from https://github.com/dstreett/FLASH2. Bedgraph and Gene Transfer Format (GTF) generated from the analysis of the Hfq CLASH, RNA-seq and TEX RNA-seq data (Thomason et al., 2015) are available from the Granneman lab DataShare repository (https://datashare.is.ed.ac.uk/handle/10283/2915).
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Hfq CLASH uncovers sRNA-target interaction networks involved in adaptation to nutrient availabilityNCBI Gene Expression Omnibus, GSE123050.
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Hfq CLASH and TEX processed datahttps://doi.org/10.7488/ds/2537.
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MS2-affinity purification coupled with RNA sequencing (MAPS) reveals GcvB sRNA targetome.NCBI Gene Expression Omnibus, GSE80019.
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Specific and pleiotropic patterns of mRNA regulation by ArcZNCBI Gene Expression Omnibus, GSE17771.
Article and author information
Author details
Ira Alexandra Iosub
Stuart William McKellar
Funding
Wellcome (102334)
- Ira Alexandra Iosub
Wellcome (091549)
- Sander Granneman
Medical Research Council (MR/R008205/1)
- Sander Granneman
Australian National Health (GNT1067241)
- Jai J Tree
Australian Medical Research Council (GNT1139313)
- Jai J Tree
Axonomix (N/A)
- Gabriella Viero
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Joseph T Wade, Wadsworth Center, New York State Department of Health, United States
Version history
- Received: December 21, 2019
- Accepted: April 30, 2020
- Accepted Manuscript published: May 1, 2020 (version 1)
- Version of Record published: May 11, 2020 (version 2)
Copyright
© 2020, Iosub et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
eLife 9:e54655.
https://doi.org/10.7554/eLife.54655
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