ArticleGenes & development2015
Molecular mechanisms of ribosomal protein gene coregulation.
Article in Genes & development, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed, 147 citations in OpenAlex.
- Divergent SAGA complexes shape the Toxoplasma transcriptome for lytic cycle progression and host interaction.Nature communications · 2026Article
- An intricate functional relationship between NuA4 and Sfp1 regulates ribosome biogenesis in response to nutrient availability.The Journal of biological chemistry · 2026Article
- Regulation of the Growth-Inhibitory Activity of Fhl1 via Interaction With Ifh1 and Crf1 at the Ribosomal Protein Gene Promoters in Saccharomyces cerevisiae.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- Comprehensive profiling of chromatin occupancy dynamics through the cell cycle.Nucleic acids research · 2026Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- Genome-Wide Detection of Leukemia Biomarkers from lincRNA-Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure.Current issues in molecular biology · 2025Article
- Histone Acetyltransferases Gcn5 and Esa1 Regulate Occupancy of RSC to Maintain Nucleosome-Depleted Regions and Promote RSC Recruitment to Coding Regions Genome-Wide inMolecular and cellular biology · 2025Article
- Ribosome Structural Changes Dynamically Affect Ribosome Function.International journal of molecular sciences · 2024Review
- Article
- Hmo1: A versatile member of the high mobility group box family of chromosomal architecture proteins.World journal of biological chemistry · 2024Review
- Cryptosporidium life cycle small molecule probing implicates translational repression and an Apetala 2 transcription factor in macrogamont differentiation.PLoS pathogens · 2024Article
- Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation inProceedings of the National Academy of Sciences of the United States of America · 2023Article
- SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid.The Journal of cell biology · 2023Article
- Enhanced gene regulation by cooperation between mRNA decay and gene transcription.Biochimica et biophysica acta. Gene regulatory mechanisms · 2023Article
- Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.iScience · 2023Article
- Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation inbioRxiv : the preprint server for biology · 2023Article
- Differential requirements for Gcn5 and NuA4 HAT activities in the starvation-induced versus basal transcriptomes.Nucleic acids research · 2023Article
- Review
- Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis.Molecular and cellular biology · 2023Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The 137 ribosomal protein genes (RPGs) of Saccharomyces provide a model for gene coregulation. We examined the positional and functional organization of their regulators (Rap1 [repressor activator protein 1], Fhl1, Ifh1, Sfp1, and Hmo1), the transcription machinery (TFIIB, TFIID, and RNA polymerase II), and chromatin at near-base-pair resolution using ChIP-exo, as RPGs are coordinately reprogrammed. Where Hmo1 is enriched, Fhl1, Ifh1, Sfp1, and Hmo1 cross-linked broadly to promoter DNA in an RPG-specific manner and demarcated by general minor groove widening. Importantly, Hmo1 extended 20-50 base pairs (bp) downstream from Fhl1. Upon RPG repression, Fhl1 remained in place. Hmo1 dissociated, which was coupled to an upstream shift of the +1 nucleosome, as reflected by the Hmo1 extension and core promoter region. Fhl1 and Hmo1 may create two regulatable and positionally distinct barriers, against which chromatin remodelers position the +1 nucleosome into either an activating or a repressive state. Consistent with in vitro studies, we found that specific TFIID subunits, in addition to cross-linking at the core promoter, made precise cross-links at Rap1 sites, which we interpret to reflect native Rap1-TFIID interactions. Our findings suggest how sequence-specific DNA binding regulates nucleosome positioning and transcription complex assembly >300 bp away and how coregulation coevolved with coding sequences.
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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.