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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 [RIF-seq] |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Experiment type |
Expression profiling by high throughput sequencing
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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
RNA sequencing of Salmonella (SL1344) in early stationary phase over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq)
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| Web link |
https://0-doi-org.brum.beds.ac.uk/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 missing |
Has this study been published? Please login to update or notify GEO. |
| 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) |
| GPL17070 |
Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium) |
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| Samples (120)
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| GSM7440488 |
WT, 8 min, biol rep 1 (Sample 16) |
| GSM7440489 |
WT, 16 min, biol rep 1 (Sample 17) |
| GSM7440490 |
ΔcspCE, 0 min, biol rep 1 (Sample 18) |
| GSM7440491 |
ΔcspCE, 2 min, biol rep 1 (Sample 19) |
| GSM7440492 |
ΔcspCE, 4 min, biol rep 1 (Sample 20) |
| GSM7440493 |
ΔcspCE, 8 min, biol rep 1 (Sample 21) |
| GSM7440494 |
ΔcspCE, 16 min, biol rep 1 (Sample 22) |
| GSM7440495 |
WT, 0 min, biol rep 2 (Sample 23) |
| GSM7440496 |
WT, 2 min, biol rep 2 (Sample 24) |
| GSM7440497 |
WT, 4 min, biol rep 2 (Sample 25) |
| GSM7440498 |
WT, 8 min, biol rep 2 (Sample 26) |
| GSM7440499 |
WT, 16 min, biol rep 2 (Sample 27) |
| GSM7440500 |
ΔcspCE, 0 min, biol rep 2 (Sample 28) |
| GSM7440501 |
ΔcspCE, 2 min, biol rep 2 (Sample 29) |
| GSM7440502 |
ΔcspCE, 4 min, biol rep 2 (Sample 30) |
| GSM7440503 |
ΔcspCE, 8 min, biol rep 2 (Sample 31) |
| GSM7440504 |
ΔcspCE, 16 min, biol rep 2 (Sample 32) |
| GSM7440505 |
WT, 0 min, biol rep 3 (Sample 33) |
| GSM7440506 |
WT, 2 min, biol rep 3 (Sample 34) |
| GSM7440507 |
WT, 4 min, biol rep 3 (Sample 35) |
| GSM7440508 |
WT, 8 min, biol rep 3 (Sample 36) |
| GSM7440509 |
WT, 16 min, biol rep 3 (Sample 37) |
| GSM7440510 |
ΔcspCE, 0 min, biol rep 3 (Sample 38) |
| GSM7440511 |
ΔcspCE, 2 min, biol rep 3 (Sample 39) |
| GSM7440512 |
ΔcspCE, 4 min, biol rep 3 (Sample 40) |
| GSM7440513 |
ΔcspCE, 8 min, biol rep 3 (Sample 41) |
| GSM7440514 |
ΔcspCE, 16 min, biol rep 3 (Sample 42) |
| GSM7440515 |
WT, 0 min, biol rep 1 (Sample 43) |
| GSM7440516 |
WT, 3 min, biol rep 1 (Sample 44) |
| GSM7440517 |
WT, 6 min, biol rep 1 (Sample 45) |
| GSM7440518 |
WT, 12 min, biol rep 1 (Sample 46) |
| GSM7440519 |
WT, 24 min, biol rep 1 (Sample 47) |
| GSM7440520 |
ΔproQ, 0 min, biol rep 1 (Sample 48) |
| GSM7440521 |
ΔproQ, 3 min, biol rep 1 (Sample 49) |
| GSM7440522 |
ΔproQ, 6 min, biol rep 1 (Sample 50) |
| GSM7440523 |
ΔproQ, 12 min, biol rep 1 (Sample 51) |
| GSM7440524 |
ΔproQ, 24 min, biol rep 1 (Sample 52) |
| GSM7440525 |
proQ++, 0 min, biol rep 1 (Sample 53) |
| GSM7440526 |
proQ++, 3 min, biol rep 1 (Sample 54) |
| GSM7440527 |
proQ++, 6 min, biol rep 1 (Sample 55) |
| GSM7440528 |
proQ++, 12 min, biol rep 1 (Sample 56) |
| GSM7440529 |
proQ++, 24 min, biol rep 1 (Sample 57) |
| GSM7440530 |
WT, 0 min, biol rep 2 (Sample 58) |
| GSM7440531 |
WT, 3 min, biol rep 2 (Sample 59) |
| GSM7440532 |
WT, 6 min, biol rep 2 (Sample 60) |
| GSM7440533 |
WT, 12 min, biol rep 2 (Sample 61) |
| GSM7440534 |
WT, 24 min, biol rep 2 (Sample 62) |
| GSM7440535 |
ΔproQ, 0 min, biol rep 2 (Sample 63) |
| GSM7440536 |
ΔproQ, 3 min, biol rep 2 (Sample 64) |
| GSM7440537 |
ΔproQ, 6 min, biol rep 2 (Sample 65) |
| GSM7440538 |
ΔproQ, 12 min, biol rep 2 (Sample 66) |
| GSM7440539 |
ΔproQ, 24 min, biol rep 2 (Sample 67) |
| GSM7440540 |
proQ++, 0 min, biol rep 2 (Sample 68) |
| GSM7440541 |
proQ++, 3 min, biol rep 2 (Sample 69) |
| GSM7440542 |
proQ++, 6 min, biol rep 2 (Sample 70) |
| GSM7440543 |
proQ++, 12 min, biol rep 2 (Sample 71) |
| GSM7440544 |
proQ++, 24 min, biol rep 2 (Sample 72) |
| GSM7440545 |
WT, 0 min, biol rep 3 (Sample 73) |
| GSM7440546 |
WT, 3 min, biol rep 3 (Sample 74) |
| GSM7440547 |
WT, 6 min, biol rep 3 (Sample 75) |
| GSM7440548 |
WT, 12 min, biol rep 3 (Sample 76) |
| GSM7440549 |
WT, 24 min, biol rep 3 (Sample 77) |
| GSM7440550 |
ΔproQ, 0 min, biol rep 3 (Sample 78) |
| GSM7440551 |
ΔproQ, 3 min, biol rep 3 (Sample 79) |
| GSM7440552 |
ΔproQ, 6 min, biol rep 3 (Sample 80) |
| GSM7440553 |
ΔproQ, 12 min, biol rep 3 (Sample 81) |
| GSM7440554 |
ΔproQ, 24 min, biol rep 3 (Sample 82) |
| GSM7440555 |
proQ++, 0 min, biol rep 3 (Sample 83) |
| GSM7440556 |
proQ++, 3 min, biol rep 3 (Sample 84) |
| GSM7440557 |
proQ++, 6 min, biol rep 3 (Sample 85) |
| GSM7440558 |
proQ++, 12 min, biol rep 3 (Sample 86) |
| GSM7440559 |
proQ++, 24 min, biol rep 3 (Sample 87) |
| GSM7440560 |
WT, 0 min, biol rep 4 (Sample 88) |
| GSM7440561 |
WT, 3 min, biol rep 4 (Sample 89) |
| GSM7440562 |
WT, 6 min, biol rep 4 (Sample 90) |
| GSM7440563 |
WT, 12 min, biol rep 4 (Sample 91) |
| GSM7440564 |
WT, 24 min, biol rep 4 (Sample 92) |
| GSM7440565 |
ΔproQ, 0 min, biol rep 4 (Sample 93) |
| GSM7440566 |
ΔproQ, 3 min, biol rep 4 (Sample 94) |
| GSM7440567 |
ΔproQ, 6 min, biol rep 4 (Sample 95) |
| GSM7440568 |
ΔproQ, 12 min, biol rep 4 (Sample 96) |
| GSM7440569 |
ΔproQ, 24 min, biol rep 4 (Sample 97) |
| GSM7440570 |
proQ++, 0 min, biol rep 4 (Sample 98) |
| GSM7440571 |
proQ++, 3 min, biol rep 4 (Sample 99) |
| GSM7440572 |
proQ++, 6 min, biol rep 4 (Sample 100) |
| GSM7440573 |
proQ++, 12 min, biol rep 4 (Sample 101) |
| GSM7440574 |
proQ++, 24 min, biol rep 4 (Sample 102) |
| GSM7440575 |
WT, 0 min, biol rep 5 (Sample 103) |
| GSM7440576 |
WT, 3 min, biol rep 5 (Sample 104) |
| GSM7440577 |
WT, 6 min, biol rep 5 (Sample 105) |
| GSM7440578 |
WT, 12 min, biol rep 5 (Sample 106) |
| GSM7440579 |
WT, 24 min, biol rep 5 (Sample 107) |
| GSM7440580 |
ΔproQ, 0 min, biol rep 5 (Sample 108) |
| GSM7440581 |
ΔproQ, 3 min, biol rep 5 (Sample 109) |
| GSM7440582 |
ΔproQ, 6 min, biol rep 5 (Sample 110) |
| GSM7440583 |
ΔproQ, 12 min, biol rep 5 (Sample 111) |
| GSM7440584 |
ΔproQ, 24 min, biol rep 5 (Sample 112) |
| GSM7440585 |
proQ++, 0 min, biol rep 5 (Sample 113) |
| GSM7440586 |
proQ++, 3 min, biol rep 5 (Sample 114) |
| GSM7440587 |
proQ++, 6 min, biol rep 5 (Sample 115) |
| GSM7440588 |
proQ++, 12 min, biol rep 5 (Sample 116) |
| GSM7440589 |
proQ++, 24 min, biol rep 5 (Sample 117) |
| GSM7440590 |
WT, 0 min, biol rep 6 (Sample 118) |
| GSM7440591 |
WT, 3 min, biol rep 6 (Sample 119) |
| GSM7440592 |
WT, 6 min, biol rep 6 (Sample 120) |
| GSM7440593 |
WT, 12 min, biol rep 6 (Sample 121) |
| GSM7440594 |
WT, 24 min, biol rep 6 (Sample 122) |
| GSM7440595 |
ΔproQ, 0 min, biol rep 6 (Sample 123) |
| GSM7440596 |
ΔproQ, 3 min, biol rep 6 (Sample 124) |
| GSM7440597 |
ΔproQ, 6 min, biol rep 6 (Sample 125) |
| GSM7440598 |
ΔproQ, 12 min, biol rep 6 (Sample 126) |
| GSM7440599 |
ΔproQ, 24 min, biol rep 6 (Sample 127) |
| GSM7440600 |
proQ++, 0 min, biol rep 6 (Sample 128) |
| GSM7440601 |
proQ++, 3 min, biol rep 6 (Sample 129) |
| GSM7440602 |
proQ++, 6 min, biol rep 6 (Sample 130) |
| GSM7440603 |
proQ++, 12 min, biol rep 6 (Sample 131) |
| GSM7440604 |
proQ++, 24 min, biol rep 6 (Sample 132) |
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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 |
PRJNA979187 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE234009_cspCE_htseq.csv.gz |
235.2 Kb |
(ftp)(http) |
CSV |
| GSE234009_proQ_htseq.csv.gz |
669.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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