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A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast

ABSTRACT: A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast

PROVIDER: PRJNA789657 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17250500.fastq.gz	Fastqsanger.gz
	SRR17250501.fastq.gz	Fastqsanger.gz
	SRR17250502.fastq.gz	Fastqsanger.gz
	SRR17250503.fastq.gz	Fastqsanger.gz
	SRR17250504.fastq.gz	Fastqsanger.gz

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A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast

Project description:Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions. Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and mRNA turnover in the cytoplasm. On a global basis, same-gene 3’ mRNA isoforms with > two-fold differences in half-lives have steady-state mRNA levels that differ by significantly less than a factor of two. In addition, increased efficiency of cleavage/polyadenylation at a specific site is associated with reduced stability of the corresponding 3’ mRNA isoform. This inverse relationship between cleavage/polyadenylation and mRNA isoform half-life reduces the variability in the steady-state levels of mRNA isoforms, and it occurs in all four growth conditions tested. These observations suggest that during cleavage/polyadenylation in the nucleus, mRNA isoforms are marked in a manner that persists upon translocation to the cytoplasm and affects the activity of mRNA degradation machinery, thus influencing mRNA stability.

2022-02-02 | GSE191091 | GEO

A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast.

Project description:Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions. Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and messenger RNA (mRNA) turnover in the cytoplasm. On a global basis, same-gene 3' mRNA isoforms with twofold or greater differences in half-lives have steady-state mRNA levels that differ by significantly less than a factor of 2. In addition, increased efficiency of cleavage/polyadenylation at a specific site is associated with reduced stability of the corresponding 3' mRNA isoform. This inverse relationship between cleavage/polyadenylation and mRNA isoform half-life reduces the variability in the steady-state levels of mRNA isoforms, and it occurs in all four growth conditions tested. These observations suggest that during cleavage/polyadenylation in the nucleus, mRNA isoforms are marked in a manner that persists upon translocation to the cytoplasm and affects the activity of mRNA degradation machinery, thus influencing mRNA stability.

| S-EPMC8794773 | biostudies-literature

Growth rate controls mRNA turnover in steady and non-steady states.

Project description:Gene expression has been investigated in relation with growth rate in the yeast Saccharomyces cerevisiae, following different experimental strategies. The expression of some specific gene functional categories increases or decreases with growth rate. Our recently published results have unveiled that these changes in mRNA concentration with growth depend on the relative alteration of mRNA synthesis and decay, and that, in addition to this gene-specific transcriptomic signature of growth, global mRNA turnover increases with growth rate. We discuss here these results in relation with other previous and concurrent publications, and we add new evidence which indicates that growth rate controls mRNA turnover even under non-steady-state conditions.

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Transcriptome reprogramming via Tob2-promoted global mRNA turnover

Project description:Transcriptome reprogramming via Tob2-promoted global mRNA turnover

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Project description:Transcriptome reprogramming via Tob2-promoted global mRNA turnover

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Heat shock induces silent ribosomes and reorganizes mRNA turnover

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Spt6 association with RNAPII directs mRNA turnover during transcription

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Transcriptome reprogramming via Tob2-promoted global mRNA turnover

Project description:We found that multilayered phosphorylation of human Tob2 modulates its PABP-binding ability to change global deadenylation and mRNA turnover, which in turn reprograms transcriptome to influence cell proliferation.

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Chromatin based modeling of transcription rates identifies the contribution of different regulatory layers to steady-state mRNA levels.

Project description:Messenger RNA levels in eukaryotes are balanced by two consecutive regulatory layers. Primary, transcriptional regulation at the level of chromatin and secondary, post-transcriptional regulation of the initial transcript in the cytoplasm. Each layer is individually studied in mechanistic detail, while integration of both processes is required to quantify the individual contribution to steady-state RNA levels. Here we show that chromatin features are sufficient to model transcription rate but with different sensitivities in dividing versus post mitotic cells. In both cases chromatin derived transcript levels explains over 80% of variance in measured RNA level enabling to separate transcription from different post-transcriptional processes. By further inclusion of measurements of mRNA half-life and micro RNA expression data we identify a low quantitative contribution of RNA decay by either micro RNA or general differential turnover to final mRNA levels. Together this establishes a chromatin based quantitative model for the contribution of transcriptional and posttranscriptional processes to steady-state levels of messenger RNA. Strand specific expression profiling by high throughput sequencing.

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