ArticlePLoS genetics2011
Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 56 papers, 1 of them a synthesis that pooled it.
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it, 101 citations in OpenAlex.
- The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons.Nucleic acids research · 2016Pooled it
- Yippee-like protein Moh1 links gene expression to metabolism and selective stress resistance inMicrobial cell (Graz, Austria) · 2026Article
- The chronODE framework for modelling multi-omic time series with ordinary differential equations and machine learning.Nature communications · 2025Article
- Global changes in synthesis rates and mRNA stabilities during adaptive responses to cell wall stress in yeast.Scientific reports · 2025Article
- Decay drives RNA abundance regulation using three distinct regulatory mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b.Life science alliance · 2024Article
- Homeostasis of mRNA concentrations through coupling transcription, export, and degradation.iScience · 2024Article
- Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- RNA Pol II Assembly Affects ncRNA Expression.International journal of molecular sciences · 2023Article
- The circular logic of mRNA homeostasis.Transcription · 2023Review
- Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts.bioRxiv : the preprint server for biology · 2023Article
- Enhanced gene regulation by cooperation between mRNA decay and gene transcription.Biochimica et biophysica acta. Gene regulatory mechanisms · 2023Article
- RNA-controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and a novel mRNA decay pathway.Nature communications · 2022Article
- Transcription feedback dynamics in the wake of cytoplasmic mRNA degradation shutdown.Nucleic acids research · 2022Article
- The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P Phosphatase Rtr1 and Influences mRNA Decay inInternational journal of molecular sciences · 2022Article
- Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.RNA biology · 2021Article
- Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data.BMC biology · 2021Article
- Review
- The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions.The Journal of biological chemistry · 2020Article
- RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters.PLoS pathogens · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome dynamics is governed by two opposing processes, mRNA production and degradation. Recent studies found that changes in these processes are frequently coordinated and that the relationship between them shapes transcriptome kinetics. Specifically, when transcription changes are counter-acted with changes in mRNA stability, transient fast-relaxing transcriptome kinetics is observed. A possible molecular mechanism underlying such coordinated regulation might lay in two RNA polymerase (Pol II) subunits, Rpb4 and Rpb7, which are recruited to mRNAs during transcription and later affect their degradation in the cytoplasm. Here we used a yeast strain carrying a mutant Pol II which poorly recruits these subunits. We show that this mutant strain is impaired in its ability to modulate mRNA stability in response to stress. The normal negative coordinated regulation is lost in the mutant, resulting in abnormal transcriptome profiles both with respect to magnitude and kinetics of responses. These results reveal an important role for Pol II, in regulation of both mRNA synthesis and degradation, and also in coordinating between them. We propose a simple model for production-degradation coupling that accounts for our observations. The model shows how a simple manipulation of the rates of co-transcriptional mRNA imprinting by Pol II may govern genome-wide transcriptome kinetics in response to environmental changes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.