期刊
EMBO JOURNAL
卷 36, 期 3, 页码 374-387出版社
WILEY
DOI: 10.15252/embj.201694639
关键词
CLIP-Seq; CRAC; EHEC; enterohaemorrhagic E. coli; non-coding RNA
资金
- Australian National Health and Medical Research Council [APP1067241]
- Wellcome Trust funding [WT090231MA, 077248]
- BBSRC Institute [BB/J004227/1]
- Wellcome Trust core funding [092076]
- Wellcome Trust [097383]
- MRC
- Australian Government NCRIS scheme
- New South Wales State Government RAAP scheme
- BBSRC [BBS/E/D/20231761, BBS/E/D/20002173] Funding Source: UKRI
- MRC [MC_UU_12018/23] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BBS/E/D/20002173, BBS/E/D/20231761] Funding Source: researchfish
- Medical Research Council [MC_UU_12018/23] Funding Source: researchfish
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 pathotypespecific 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.
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