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| Status |
Public on Mar 26, 2024 |
| Title |
Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq] |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Experiment type |
Other
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| Summary |
RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half-life in Salmonella in early stationary phase is less than 1 minute, a third of previous estimates. We found that over half of the 500 most long-lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with CLIP-seq revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for both proteins in the control of respiration, and for ProQ in the oxidative stress response. Our findings provide new insights into post-transcriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.
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| Overall design |
Sample 1-12: CLIP-seq, Sample 13-132 RIF-seq
Cross-linking immunoprecipitation-high-throughput sequencing (CLIP-seq) to detect CspC and CspE binding sites in Salmonella (SL1344)
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| Web link |
https://doi.org/10.1073/pnas.2308814121
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| Contributor(s) |
Jenniches L, Michaux C, Popella L, Reichardt S, Vogel J, Westermann AJ, Barquist L |
| Citation(s) |
38527194 |
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| Submission date |
Jun 02, 2023 |
| Last update date |
May 13, 2024 |
| Contact name |
Laura Jenniches |
| E-mail(s) |
laura.jenniches@helmholtz-hiri.de
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| Organization name |
Helmholtz Institute for RNA-based Infection Research
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| Street address |
Josef-Schneider-Straße 2/D15
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| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platforms (1) |
| GPL21220 |
Illumina NextSeq 500 (Salmonella enterica subsp. enterica serovar Typhimurium) |
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| Samples (12)
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| GSM7440455 |
CspC CLIP-seq, UV-crosslinked, biol rep 1 (Sample 1) |
| GSM7440456 |
CspC CLIP-seq, not UV-crosslinked, biol rep 1 (Sample 2) |
| GSM7440457 |
CspC CLIP-seq, UV-crosslinked, biol rep 2 (Sample 3) |
| GSM7440458 |
CspC CLIP-seq, not UV-crosslinked, biol rep 2 (Sample 4) |
| GSM7440459 |
CspC CLIP-seq, UV-crosslinked, biol rep 3 (Sample 5) |
| GSM7440460 |
CspC CLIP-seq, not UV-crosslinked, biol rep 3 (Sample 6) |
| GSM7440461 |
CspE CLIP-seq, UV-crosslinked, biol rep 1 (Sample 7) |
| GSM7440462 |
CspE CLIP-seq, not UV-crosslinked, biol rep 1 (Sample 8) |
| GSM7440463 |
CspE CLIP-seq, UV-crosslinked, biol rep 2 (Sample 9) |
| GSM7440464 |
CspE CLIP-seq, not UV-crosslinked, biol rep 2 (Sample 10) |
| GSM7440465 |
CspE CLIP-seq, UV-crosslinked, biol rep 3 (Sample 11) |
| GSM7440466 |
CspE CLIP-seq, not UV-crosslinked, biol rep 3 (Sample 12) |
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| This SubSeries is part of SuperSeries: |
| GSE234010 |
Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives |
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| Relations |
| BioProject |
PRJNA979180 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE234007_CspC_counts.csv.gz |
147.1 Kb |
(ftp)(http) |
CSV |
| GSE234007_CspE_counts.csv.gz |
177.9 Kb |
(ftp)(http) |
CSV |
| GSE234007_cspC_CLIP_peaks.gff.gz |
215.2 Kb |
(ftp)(http) |
GFF |
| GSE234007_cspE_CLIP_peaks.gff.gz |
264.9 Kb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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