Projects per year
Abstract
RNA sequencing studies have identified hundreds of non-coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high-throughput analysis of RNA-RNA interactions in bacteria. Here we demonstrate that in vivo sRNA-mRNA duplexes can be recovered using UV-crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base-paired sRNA-mRNA duplexes in association with RNase E, allowing proximity-dependent ligation and sequencing of cognate sRNA-mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA-mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co-regulated target mRNAs. We identified multiple mRNA targets for the pathotype-specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli Numerous sRNA interactions were also identified with non-coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome.
Original language | English |
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Pages (from-to) | 374-387 |
Journal | EMBO Journal |
Volume | 36 |
Issue number | 3 |
Early online date | 11 Nov 2016 |
DOIs | |
Publication status | Published - 1 Feb 2017 |
Keywords / Materials (for Non-textual outputs)
- CLIP-Seq
- CRAC
- EHEC
- enterohaemorrhagic E. coli
- non-coding RNA
Fingerprint
Dive into the research topics of 'Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E'. Together they form a unique fingerprint.Projects
- 5 Finished
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FUNCTIONAL CONSEQUENCES OF SYNONOMOUS MUTATIONS IN EUKARYOTIC CELLS
Kudla, G. (Principal Investigator)
1/08/12 → 31/01/18
Project: Research
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Innate immunity and endemic diseases in livestock species
Collie, D. (Principal Investigator), Beard, P. (Co-investigator), Bishop, S. (Co-investigator), Bronsvoort, M. (Co-investigator), Burt, D. (Co-investigator), Fitzgerald, R. (Co-investigator), Freeman, T. (Co-investigator), Gally, D. (Co-investigator), Gill, A. (Co-investigator), Glass, E. (Co-investigator), Hocking, P. (Co-investigator), Hope, J. (Co-investigator), Hume, D. (Co-investigator), Kaiser, P. (Co-investigator), Mabbott, N. (Co-investigator), McLachlan, G. (Co-investigator), Morrison, L. (Co-investigator), Stevens, J. (Co-investigator), Stevens, M. (Co-investigator) & Watson, M. (Co-investigator)
1/04/12 → 31/03/17
Project: Research
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Kinetic changes in RNA surveillance and non-coding RNA function during nutrition downshift
Tollervey, D. (Principal Investigator)
1/10/11 → 31/03/17
Project: Research
Profiles
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David Gally
- Royal (Dick) School of Veterinary Studies - Personal Chair of Microbial Genetics
Person: Academic: Research Active
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Grzegorz Kudla
- Deanery of Molecular, Genetic and Population Health Sciences - Personal Chair of Genetic Engineering
- MRC Human Genetics Unit
Person: Academic: Research Active , Academic: Research Active (Research Assistant)