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

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

PROVIDER: PRJNA979180 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24806606_1.fastq.gz	Fastqsanger.gz
	SRR24806606_2.fastq.gz	Fastqsanger.gz
	SRR24806607_1.fastq.gz	Fastqsanger.gz
	SRR24806607_2.fastq.gz	Fastqsanger.gz
	SRR24806608_1.fastq.gz	Fastqsanger.gz

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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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