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Retapamullin and Chloramphenicol treated mRNA half-life profiling.

ABSTRACT: Retapamullin and Chloramphenicol treated mRNA half-life profiling.

PROVIDER: PRJNA950406 | ENA |

REPOSITORIES: ENA

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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.

2023-04-03 | GSE228591 | GEO

Cell cycle mRNA half-life profiling.

Project description:Cell cycle mRNA half-life profiling.

| PRJNA950409 | ENA

BR-body mutant mRNA half-life profiling.

Project description:BR-body mutant mRNA half-life profiling.

| PRJNA551694 | ENA

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

WT, ∆rhlB and ∆rppH mRNA half-life profiling.

Project description:WT, ∆rhlB and ∆rppH mRNA half-life profiling.

| PRJNA950407 | ENA

Whole genome analysis of mRNA decay in P. falciparum reveals a lengthening of mRNA half-life during the IDC

Project description:The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms. Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiological role, and plays an important role in determining levels of gene expression. We have used a genome wide approach to characterize mRNA decay in Plasmodium falciparum. We found that globally, rates of mRNA decay increase dramatically during the asexual intraerythrocytic developmental cycle. During the ring stage of the cycle, the average mRNA half-life was 9.5 minutes, yet this was extended to an average of 65 minutes during the late schizont stage of development. Thus a major determinant of mRNA decay rate appears to be linked to the stage of intraerythrocytic development. Furthermore, we have found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening. These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes. Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies. Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intraerythrocytic development. This type of genome wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum. Keywords: Plasmodium falciparum treated with actinomycin D

2007-07-19 | GSE8099 | GEO

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

WT and RNE∆IDR mRNA half-life profiling in Sinorhizobium meliloti.

Project description:WT and RNE∆IDR mRNA half-life profiling in Sinorhizobium meliloti.

| PRJNA1055090 | ENA

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

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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