ArticlePLoS genetics2009
Regulon-specific control of transcription elongation across the yeast genome.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it, 76 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
- Beyond the ORF: Paralog-specific regulation of RPS7/eS7 mRNAs via 3'-UTRs and promoter sequences.PloS one · 2025Article
- Regulation of transcription elongation anticipates alternative gene expression strategies across the cell cycle.PloS one · 2025Article
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- Advances inJournal of fungi (Basel, Switzerland) · 2023Review
- Multifaceted Roles of ICP22/ORF63 Proteins in the Life Cycle of Human Herpesviruses.Frontiers in microbiology · 2021Review
- The role of FACT in managing chromatin: disruption, assembly, or repair?Nucleic acids research · 2020Review
- Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis inRNA (New York, N.Y.) · 2020Article
- The telomeric Cdc13-Stn1-Ten1 complex regulates RNA polymerase II transcription.Nucleic acids research · 2019Article
- Article
- Feedback regulation of ribosome assembly.Current genetics · 2018Review
- The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation.Nucleic acids research · 2017Article
- Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo.Nucleic acids research · 2017Article
- The importance of controlling mRNA turnover during cell proliferation.Current genetics · 2016Review
- Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization.Molecular cell · 2016Article
- Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex.Cell reports · 2016Article
- Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.Nucleic acids research · 2015Article
- Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae.BMC genomics · 2014Article
- Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.RNA biology · 2014Article
- Cytoplasmic 5'-3' exonuclease Xrn1p is also a genome-wide transcription factor in yeast.Frontiers in genetics · 2014Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription elongation by RNA polymerase II was often considered an invariant non-regulated process. However, genome-wide studies have shown that transcriptional pausing during elongation is a frequent phenomenon in tightly-regulated metazoan genes. Using a combination of ChIP-on-chip and genomic run-on approaches, we found that the proportion of transcriptionally active RNA polymerase II (active versus total) present throughout the yeast genome is characteristic of some functional gene classes, like those related to ribosomes and mitochondria. This proportion also responds to regulatory stimuli mediated by protein kinase A and, in relation to cytosolic ribosomal-protein genes, it is mediated by the silencing domain of Rap1. We found that this inactive form of RNA polymerase II, which accumulates along the full length of ribosomal protein genes, is phosphorylated in the Ser5 residue of the CTD, but is hypophosphorylated in Ser2. Using the same experimental approach, we show that the in vivo-depletion of FACT, a chromatin-related elongation factor, also produces a regulon-specific effect on the expression of the yeast genome. This work demonstrates that the regulation of transcription elongation is a widespread, gene class-dependent phenomenon that also affects housekeeping genes.
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Registered trials
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.