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| Status |
Public on Jun 19, 2019 |
| Title |
Hfq Globally Binds and Destabilizes sRNAs and mRNAs in Yersinia pestis |
| Organism |
Yersinia pestis |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. pestis and that Hfq also globally binds noncoding small RNAs (sRNAs) encoded by the intergenic, antisense, and 3′ regions of mRNAs. An Hfq U-rich stretch is highly enriched in sRNAs, while motifs partially complementary to AGAAUAA and GGGGAUUA are enriched in both mRNAs and sRNAs. Hfq-binding motifs are enriched at both terminal sites and in the gene body of mRNAs. Surprisingly, a large fraction of the sRNA and mRNA regions bound by Hfq and those downstream are destabilized, likely via a 5′P-activated RNase E degradation pathway, which is consistent with a model in which Hfq facilitates sRNA-mRNA base pairing and the coupled degradation in Y. pestis. These results together have presented a high-quality Hfq-RNA interaction map in Y. pestis, which should be important for further deciphering the regulatory role of Hfq-sRNAs in Y. pestis.
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| Overall design |
Hfq-binding RNA profiles of Y. pestis wild type (WT) and hfq-flag were generated by deep sequencing using Illumina.
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| Contributor(s) |
Yang R, Zhang Y, Han Y, Chen D |
| Citation(s) |
31311844 |
| |
| Submission date |
Feb 03, 2016 |
| Last update date |
Sep 18, 2019 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
|
| Department |
Center for Genome Analysis
|
| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
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| Platforms (1) |
| GPL21403 |
Illumina Genome Analyzer IIx (Yersinia pestis) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA310777 |
| SRA |
SRP069258 |
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