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| Status |
Public on Dec 14, 2016 |
| Title |
In vivo cleavage map illuminates the central role of RNase E in coding and noncoding RNA pathways |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs, whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 3’-fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post- transcriptional regulators.
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| Overall design |
8 total RNA samples from Salmonella WT and rne-3071(rne-TS) strains grown at 28°C with and without heat treatment (44°C) for 30min, in duplicate.
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| Contributor(s) |
Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Papenfort K, Reinhardt R, Wieden H, Luisi B, Vogel J |
| Citation(s) |
28061332 |
| |
| Submission date |
May 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Li |
| Organization name |
University of California, Irvine
|
| Street address |
University of California, Irvine
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platforms (1) |
| GPL19729 |
Illumina HiSeq 2500 (Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA322828 |
| SRA |
SRP075688 |
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