Projects per year
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.
Original language | English |
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Article number | e54655 |
Number of pages | 33 |
Journal | eLIFE |
Volume | 9 |
DOIs | |
Publication status | Published - 1 May 2020 |
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Dive into the research topics of 'Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation'. Together they form a unique fingerprint.Projects
- 7 Finished
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Unravelling post-transcriptional regulatory networks in pathogenic S. aureus
1/01/18 → 22/08/23
Project: Research
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Wellcome Trust Four-Year PhD Studentship with the Cell Biology Programme (Ira Alexandra Iosub)
Beggs, J.
1/10/13 → 30/09/17
Project: Research
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Future-Proofing the sustainability of the MRC high throughput sequencing hub in Scotland
Blaxter, M.
1/10/12 → 30/09/14
Project: Research
Datasets
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Hfq CLASH and TEX processed data
Granneman, S. (Creator), Edinburgh DataShare, 30 Apr 2019
DOI: 10.7488/ds/2537, https://www.biorxiv.org/content/10.1101/481986v1
Dataset
Profiles
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Sander Granneman
- School of Biological Sciences - Personal Chair of RNA Biochemistry
- Centre for Engineering Biology
Person: Academic: Research Active