ArticleGenome research2013
Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 39 citations in OpenAlex.
- Context-dependent interplay of Swi-Snf and Tup1-Cyc8 influences chromatin and transcription at antagonistically regulated genes.Nature communications · 2026Article
- Chromosome III Aneuploidy Enhances Ethanol Tolerance in Industrial Saccharomyces cerevisiae by Increasing the TUP1 Copy Number.Microbial biotechnology · 2025Article
- The influence of flocculation upon global gene transcription in a yeastMicrobial genomics · 2024Article
- Article
- Tup1 is critical for transcriptional repression in Quiescence in S. cerevisiae.PLoS genetics · 2022Article
- Article
- Genetic analysis argues for a coactivator function for the Saccharomyces cerevisiae Tup1 corepressor.Genetics · 2021Article
- Article
- Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.PLoS computational biology · 2021Article
- A self-balancing circuit centered on MoOsm1 kinase governs adaptive responses to host-derived ROS ineLife · 2020Article
- A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning.Applied microbiology and biotechnology · 2020Article
- Cyc8p and Tup1p transcription regulators antagonistically regulate Flo11p expression and complexity of yeast colony biofilms.PLoS genetics · 2018Article
- Sas3 and Ada2(Gcn5)-dependent histone H3 acetylation is required for transcription elongation at the de-repressed FLO1 gene.Nucleic acids research · 2017Article
- The Coprinopsis cinerea Tup1 homologue Cag1 is required for gill formation during fruiting body morphogenesis.Biology open · 2016Article
- Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome.Genome research · 2016Article
- Local potentiation of stress-responsive genes by upstream noncoding transcription.Nucleic acids research · 2016Article
- Dynamic Sumoylation of a Conserved Transcription Corepressor Prevents Persistent Inclusion Formation during Hyperosmotic Stress.PLoS genetics · 2016Article
- Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity.Molecular cell · 2015Article
- BAF250a Protein Regulates Nucleosome Occupancy and Histone Modifications in Priming Embryonic Stem Cell Differentiation.The Journal of biological chemistry · 2015Article
- Nucleosome Organization in Human Embryonic Stem Cells.PloS one · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
The yeast Cyc8 (also known as Ssn6)-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Cyc8-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of CYC8 or TUP1 and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of CYC8 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Cyc8 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of CYC8 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Cyc8-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation.
Indexed as
Identifiers
What OpenQuestion holds
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.