2024/03/25 by Laura Jenniches, Charlotte Michaux, Linda Popella +4 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Bacterial Genetics and Biotechnology #Biology #Computational biology #Drosha #Gene #Gene expression #Genetics #Non-coding RNA #RNA #RNA Research and Splicing #RNA and protein synthesis mechanisms #RNA interference #RNA-binding protein #Regulation of gene expression #Small RNA #Transcriptome #Untranslated region
paper · pdf · doi:10.1073/pnas.2308814121
openalex publication_date 2024/03/25 · openalex created_date 2024/03/26 · openalex updated_date 2026/07/22
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.