ArticleNature structural & molecular biology2023
Structure of histone deacetylase complex Rpd3S bound to nucleosome.
Article in Nature structural & molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 15 citations in OpenAlex.
- Histone Acetylation Dynamics Regulate Fungal Development, Pathogenicity, and Mycotoxin Biosynthesis.Journal of fungi (Basel, Switzerland) · 2026Review
- Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.Nucleic acids research · 2026Article
- Histone modification cross-talk: analytical tools and molecular mechanisms.The Biochemical journal · 2026Review
- Chromatin context-dependent deacetylation by the asymmetric Rpd3L.Nucleic acids research · 2026Article
- Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation.Nucleic acids research · 2025Article
- Inherent asymmetry of Rpd3S coordinates its nucleosome engagement and association with elongating RNA polymerase II.Nature structural & molecular biology · 2025Article
- Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers.Nucleic acids research · 2025Article
- Histone Modification Pathways Suppressing Cryptic Transcription.Epigenomes · 2024Article
- Repression of pervasive antisense transcription is the primary role of fission yeast RNA polymerase II CTD serine 2 phosphorylation.Nucleic acids research · 2024Article
- Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers.Nucleic acids research · 2024Article
- Structures and dynamics of Rpd3S complex bound to nucleosome.Science advances · 2024Article
- Investigating Potential Cancer Therapeutics: Insight into Histone Deacetylases (HDACs) Inhibitions.Pharmaceuticals (Basel, Switzerland) · 2024Article
- Epigenetics of hypertension as a risk factor for the development of coronary artery disease in type 2 diabetes mellitus.Frontiers in endocrinology · 2024Review
- Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex.Nature communications · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is recruited to H3K36-methylated nucleosomes to suppress cryptic transcription initiation. However, how subunits of Rpd3S are assembled and coordinated to recognize nucleosomal substrates and exert their deacetylation function remains unclear. Here we report the structure of Saccharomyces cerevisiae Rpd3S deacetylase bound to H3K36me3-modified nucleosome at 3.1 Å resolution. It shows that Sin3 and Rco1 subunits orchestrate the assembly of the complex and mediate its contact with nucleosome at multiple sites, with the Sin3-DNA interface as a pivotal anchor. The PHD1 domain of Rco1 recognizes the unmodified H3K4 and places the following H3 tail toward the active site of Rpd3, while the chromodomain of Eaf3 subunit recognizes the H3K36me3 mark and contacts both nucleosomal and linker DNA. The second copy of Eaf3-Rco1 is involved in neighboring nucleosome binding. Our work unravels the structural basis of chromatin targeting and deacetylation by the Rpd3S complex.
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