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Series GSE234007 Query DataSets for GSE234007
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
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.
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)
Web link
Contributor(s) Jenniches L, Michaux C, Popella L, Reichardt S, Vogel J, Westermann AJ, Barquist L
Citation(s) 38527194
Submission date Jun 02, 2023
Last update date May 13, 2024
Contact name Laura Jenniches
Organization name Helmholtz Institute for RNA-based Infection Research
Street address Josef-Schneider-Straße 2/D15
City Würzburg
ZIP/Postal code 97080
Country Germany
Platforms (1)
GPL21220 Illumina NextSeq 500 (Salmonella enterica subsp. enterica serovar Typhimurium)
Samples (12)
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)
This SubSeries is part of SuperSeries:
GSE234010 Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives
BioProject PRJNA979180

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data are available on Series record

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