ArticlePLoS genetics2012
DNA Topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 49 citations in OpenAlex.
- DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression.bioRxiv : the preprint server for biology · 2026Article
- DNA supercoiling modulates eukaryotic transcription in a gene-orientation dependent manner.bioRxiv : the preprint server for biology · 2025Article
- Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.Nature structural & molecular biology · 2025Article
- RNA interacts with topoisomerase I to adjust DNA topology.Molecular cell · 2024Article
- DNA topology: A central dynamic coordinator in chromatin regulation.Current opinion in structural biology · 2024Review
- Downstream-of-gene (DoG) transcripts contribute to an imbalance in the cancer cell transcriptome.Science advances · 2024Article
- Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against hypertranscription.Nature communications · 2023Article
- DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes.Molecular cell · 2023Article
- Article
- Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing.Cell reports · 2021Article
- The Functional Consequences of Eukaryotic Topoisomerase 1 Interaction with G-Quadruplex DNA.Genes · 2020Review
- Article
- Topoisomerase activity is linked to altered nucleosome positioning and transcriptional regulation in the fission yeast fbp1 gene.PloS one · 2020Article
- Chemotherapeutic Drugs Inhibiting Topoisomerase 1 Activity Impede Cytokine-Induced and NF-κB p65-Regulated Gene Expression.Cancers · 2019Article
- Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae.Nucleic acids research · 2018Article
- Structure and Chromosomal Organization of Yeast Genes Regulated by Topoisomerase II.International journal of molecular sciences · 2018Review
- Physiological functions of programmed DNA breaks in signal-induced transcription.Nature reviews. Molecular cell biology · 2017Review
- Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae.Nucleic acids research · 2017Article
- Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase.PLoS genetics · 2017Article
- Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These genes are characterized by high transcriptional plasticity, chromatin regulation, TATA box presence, and enrichment of a nucleosome at a critical position in the promoter region, in line with a repressible/inducible mode of regulation. Single-gene studies with a range of genes belonging to this group demonstrate that topoisomerases play an important role during activation of these genes. Subsequent in-depth analysis of the inducible PHO5 gene reveals that topoisomerases are essential for binding of the Pho4p transcription factor to the PHO5 promoter, which is required for promoter nucleosome removal during activation. In contrast, topoisomerases are dispensable for constitutive transcription initiation and elongation of PHO5, as well as the nuclear entrance of Pho4p. Finally, we provide evidence that topoisomerases are required to maintain the PHO5 promoter in a superhelical state, which is competent for proper activation. In conclusion, our results reveal a hitherto unknown function of topoisomerases during transcriptional activation of genes with a repressible/inducible mode of regulation.
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