期刊
EMBO JOURNAL
卷 35, 期 9, 页码 991-1011出版社
WILEY
DOI: 10.15252/embj.201593360
关键词
CLIP; CsrA; Hfq; non-coding RNA; peak calling; post-transcriptional control; small RNA; terminator; translation
资金
- DFG
- Bavarian BioSysNet program
- BMBF
- EMBO
- Wenner-Gren Foundations
- Alexander von Humboldt Foundation
The molecular roles of many RNA-binding proteins in bacterial post-transcriptional gene regulation are not well understood. Approaches combining invivo UV crosslinking with RNA deep sequencing (CLIP-seq) have begun to revolutionize the transcriptome-wide mapping of eukaryotic RNA-binding protein target sites. We have applied CLIP-seq to chart the target landscape of two major bacterial post-transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single-nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3-located Rho-independent terminators as a universal motif involved in Hfq-RNA interactions. Additionally, Hfq preferentially binds 5 to sRNA-target sites in mRNAs, and 3 to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA-mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA-target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP-seq approach will bring new insights into post-transcriptional gene regulation by RNA-binding proteins in diverse bacterial species.
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