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Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives

ABSTRACT: Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives

PROVIDER: PRJNA979183 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24806900.fastq.gz	Fastqsanger.gz
	SRR24807000.fastq.gz	Fastqsanger.gz
	SRR24806901.fastq.gz	Fastqsanger.gz
	SRR24807001.fastq.gz	Fastqsanger.gz
	SRR24806902.fastq.gz	Fastqsanger.gz

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Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq]

Project description:Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq]

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Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [RIF-seq]

Project description:Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [RIF-seq]

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Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [RIF-seq]

Project description: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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Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq]

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Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives

Project description:This SuperSeries is composed of the SubSeries listed below.

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Global RNA half lives in cyanobacteria

Project description:Global RNA half lives in cyanobacteria

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Project description:We calculated global RNA half lives for all genes in the cyanobacteria Synechococcus sp. strain PCC 7002. Samples from three replicates of the WT strain were taken before and following the addition of the antibiotic rifampicin to stop nascent transcription. RNA spike-ins were added for normalization and using the number of RNA-sequencing reads we were able to calculate half lives for genes, transcripts, and for each position on the genome.

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Improved RNA stability estimation through Bayesian modeling reveals most <i>Salmonella</i> transcripts have subminute half-lives.

Project description: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 posttranscriptional 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 min, 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 cross-linking and immunoprecipitation followed by RNA sequencing (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 ProQ in the oxidative stress response. Our findings provide insights into posttranscriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.

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