Projects per year
Abstract / Description of output
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 |
---|---|
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
-
FUNCTIONAL CONSEQUENCES OF SYNONOMOUS MUTATIONS IN EUKARYOTIC CELLS
1/08/12 → 31/01/18
Project: Research
-
Innate immunity and endemic diseases in livestock species
Collie, D., Beard, P., Bishop, S., Bronsvoort, M., Burt, D., Fitzgerald, R., Freeman, T., Gally, D., Gill, A., Glass, E., Hocking, P., Hope, J., Hume, D., Kaiser, P., Mabbott, N., McLachlan, G., Morrison, L., Stevens, J., Stevens, M. & Watson, M.
1/04/12 → 31/03/17
Project: Research
-
Core funding renewal for the Wellcome Trust Centre for Cell Biology
1/10/11 → 30/04/17
Project: Research
Profiles
-
David Gally
- Royal (Dick) School of Veterinary Studies - Personal Chair of Microbial Genetics
Person: Academic: Research Active
-
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)