Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
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-asso...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2020-05-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/54655 |
| _version_ | 1811181088868925440 |
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| author | Ira Alexandra Iosub Robert Willem van Nues Stuart William McKellar Karen Jule Nieken Marta Marchioretto Brandon Sy Jai Justin Tree Gabriella Viero Sander Granneman |
| author_facet | Ira Alexandra Iosub Robert Willem van Nues Stuart William McKellar Karen Jule Nieken Marta Marchioretto Brandon Sy Jai Justin Tree Gabriella Viero Sander Granneman |
| author_sort | Ira Alexandra Iosub |
| collection | DOAJ |
| description | 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. We 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. |
| first_indexed | 2024-04-11T09:13:56Z |
| format | Article |
| id | doaj.art-66b726c8bd8c43848fc026c95cf42ec4 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:13:56Z |
| publishDate | 2020-05-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-66b726c8bd8c43848fc026c95cf42ec42022-12-22T04:32:25ZengeLife Sciences Publications LtdeLife2050-084X2020-05-01910.7554/eLife.54655Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptationIra Alexandra Iosub0https://orcid.org/0000-0002-2924-2471Robert Willem van Nues1Stuart William McKellar2https://orcid.org/0000-0003-0792-9878Karen Jule Nieken3Marta Marchioretto4Brandon Sy5Jai Justin Tree6Gabriella Viero7https://orcid.org/0000-0002-6755-285XSander Granneman8https://orcid.org/0000-0003-4387-1271Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United KingdomInstitute of Cell Biology, University of Edinburgh, Edinburgh, United KingdomCentre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United KingdomInstitute of Cell Biology, University of Edinburgh, Edinburgh, United KingdomInstitute of Biophysics, CNR Unit, Trento, ItalySchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, AustraliaSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, AustraliaInstitute of Biophysics, CNR Unit, Trento, ItalyCentre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United KingdomBy 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. We 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.https://elifesciences.org/articles/54655RNA-RNA interactionsCLASHprotein-RNA interactionsHfqnon-coding RNApost-transcriptional regulation |
| spellingShingle | Ira Alexandra Iosub Robert Willem van Nues Stuart William McKellar Karen Jule Nieken Marta Marchioretto Brandon Sy Jai Justin Tree Gabriella Viero Sander Granneman Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation eLife RNA-RNA interactions CLASH protein-RNA interactions Hfq non-coding RNA post-transcriptional regulation |
| title | Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation |
| title_full | Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation |
| title_fullStr | Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation |
| title_full_unstemmed | Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation |
| title_short | Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation |
| title_sort | hfq clash uncovers srna target interaction networks linked to nutrient availability adaptation |
| topic | RNA-RNA interactions CLASH protein-RNA interactions Hfq non-coding RNA post-transcriptional regulation |
| url | https://elifesciences.org/articles/54655 |
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