ArticleGenome biology2010
RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 60 citations in OpenAlex.
- Parasitic plasmids are anchored to inactive regions of eukaryotic chromosomes through a nucleosome signal.The EMBO journal · 2025Article
- Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks.Science advances · 2022Article
- The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand.Genome research · 2022Article
- Linking the dynamics of chromatin occupancy and transcription with predictive models.Genome research · 2021Article
- Transcription shapes genome-wide histone acetylation patterns.Nature communications · 2021Article
- Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes.Genome research · 2020Article
- New Roles for Canonical Transcription Factors in Repeat Expansion Diseases.Trends in genetics : TIG · 2020Review
- Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress-dependent mRNAs.EMBO reports · 2019Article
- Distinct types of short open reading frames are translated in plant cells.Genome research · 2019Article
- Nucleosome positions alone can be used to predict domains in yeast chromosomes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes.PLoS genetics · 2019Article
- Multiplexed gene control reveals rapid mRNA turnover.Science advances · 2017Article
- An mRNA Capping Enzyme Targets FACT to the Active Gene To Enhance the Engagement of RNA Polymerase II into Transcriptional Elongation.Molecular and cellular biology · 2017Article
- Dynamics of Nucleosome Positioning Maturation following Genomic Replication.Cell reports · 2016Article
- RNA polymerase II depletion promotes transcription of alternative mRNA species.BMC molecular biology · 2016Article
- Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization.Molecular cell · 2016Article
- Article
- Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo.G3 (Bethesda, Md.) · 2015Article
- Article
- Functional role of histone variant Htz1 in the stress response to oleate in Saccharomyces cerevisiae.Bioscience reports · 2015Article
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundThe use of genome-wide RNA abundance profiling by microarrays and deep sequencing has spurred a revolution in our understanding of transcriptional control. However, changes in mRNA abundance reflect the combined effect of changes in RNA production, processing, and degradation, and thus, mRNA levels provide an occluded view of transcriptional regulation.
resultsTo partially disentangle these issues, we carry out genome-wide RNA polymerase II (PolII) localization profiling in budding yeast in two different stress response time courses. While mRNA changes largely reflect changes in transcription, there remains a great deal of variation in mRNA levels that is not accounted for by changes in PolII abundance. We find that genes exhibiting 'excess' mRNA produced per PolII are enriched for those with overlapping cryptic transcripts, indicating a pervasive role for nonproductive or regulatory transcription in control of gene expression. Finally, we characterize changes in PolII localization when PolII is genetically inactivated using the rpb1-1 temperature-sensitive mutation. We find that PolII is lost from chromatin after roughly an hour at the restrictive temperature, and that there is a great deal of variability in the rate of PolII loss at different loci.
conclusionsTogether, these results provide a global perspective on the relationship between PolII and mRNA production in budding yeast.
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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.