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BR-body mutant mRNA half-life profiling.

ABSTRACT: BR-body mutant mRNA half-life profiling.

PROVIDER: PRJNA551694 | ENA |

REPOSITORIES: ENA

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BR-body mutant mRNA half-life profiling.

Project description:BR-body mutant strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq. JS38 (wild type) was compared to JS221 (lacking the intrinsically disordered CTD and unable to form BR-bodies), JS233 (unable to recruit degradosome components into BR-bodies), and JS299 (active site mutant of RNase E).

2019-06-29 | GSE133532 | GEO

BR-body enrichment for RNA substrate identification.

Project description:BR-body RNA substrates were identified by RNA-seq of enriched BR-body samples compared to cell lysate.

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Cell cycle mRNA half-life profiling.

Project description:mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in synchronized cells collected from different stages of the cell cycle including swarmer cells, stalk cells (45 min post synchrony), and predivisional cells (90 min post synchrony). For each cell population, transcription was disrupted by the antibiotic rifampicin, and RNA samples were collected at different time points to measure the mRNA half-lives.

2023-04-03 | GSE228593 | GEO

C. crescentus BR-body enrichment

Project description:Enriched BR-body samples (JS299) samples and negative control samples (JS221) from a strain lacking BR-bodies. BR-body enrichment was performed by differential centrifugation as in 10.1016/j.xpro.2020.100205. Each sample was collected in three biological replicates.

2022-12-13 | MSV000090894 | MassIVE

Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models

Project description:Models of MECP2 dysfunction in Rett syndrome (RTT) assume that transcription rate changes directly correlate with altered steady-state mRNA levels. However, limited evidence suggests that transcription rate changes are buffered by poorly understood compensatory post-transcriptional mechanisms. Here we measure transcription rate and mRNA half-life changes in RTT patient neurons using RATE-seq, and re-interpret nuclear and whole-cell RNAseq from Mecp2 mice. Genes are dysregulated by changing transcription rate only or half-life only and are buffered when both are changed. We utilized classifier models to understand the direction of transcription rate changes based on gene-body DNA sequence, and combined frequencies of three dinucleotides were better predictors than contributions by CA and CG. MicroRNA and RNA-Binding Protein (RBP) motifs were enriched in 3ʹUTRs of genes with half-life changes. Motifs for nuclear localized RBPs were enriched on buffered genes with increased transcription rate. Our findings identify post-transcriptional mechanisms in humans and mice that alter half-life only or buffer transcription rate changes when a transcriptional modulator gene is mutated in a neurodevelopmental disorder.

2023-01-27 | GSE191168 | GEO

Retapamullin and Chloramphenicol treated mRNA half-life profiling.

Project description:mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in cells that were inhibited in translation initiation (retapamullin) or elongation (chloramphenicol) by shutting of transcription with the antibiotic rifampicin, and following mRNA abundance at 1, 2, 4, 8, and 15 minutes post rifampicin. All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium. Two biological replicates time coursees were collected from independent starter cultures.

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BR-body enrichment for RNA substrate identification.

Project description:BR-body enrichment for RNA substrate identification.

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Half-lives mRNA analysis of Stenotrophomonas maltophilia D457 and rng-deficient mutant

Project description:We calculated half-life values of mRNAs quantified by RNA-Seq by a suitable method of normalization. We determined the half-lives of more than 2200 mRNAs in the Stenotrophomonas maltophilia D457 wild-type strain and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient mutant respectively. We found an overall enhancement of half-life times of mRNAs when the gene encoding RNase G is lacking, showing that many RNAs are targets of RNase G in S. maltophilia. For achieving such goal, we propose a method for the normalization of RNA-Seq based studies on global bacterial mRNA decay.

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mRNA structure regulates protein expression through changes in functional half-life

Project description:mRNA structure regulates protein expression through changes in functional half-life

| PRJNA578697 | ENA

NANOS2-binding regulates mRNA half-life and key spermatogonial stem cell self-renewal pathways

Project description:We have identified NANOS2 bound targets transcriptome wide by employing CRAC and RNA-seq in mouse SSCs. We have determined the average mRNA half-life in SSCs by SLAM-seq. By comparing CRAC and SLAM-seq datasets, we have demonstrated that NANOS2 binding reduces mRNA stability in SSCs.

2021-05-06 | GSE149835 | GEO

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