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TitleChromatin context-dependent deacetylation by the asymmetric Rpd3L.
Journal, issue, pagesNucleic Acids Res, Vol. 54, Issue 9, Year 2026
Publish dateMay 5, 2026
AuthorsHeyu Zhao / Huadong Li / Chi Wang / Xuechen Yang / Binqian Zou / Shuqi Dong / Nan Zhang / Yuxing Zhou / Li Yi / Ying Zhang / Yixuan Xie / Dajiang Qin / William Chong Hang Chao / Duanqing Pei / Jun He /
PubMed AbstractThe regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone ...The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone deacetylase complex (HDAC) that dynamically adapt to chromatin states to reinforce transcriptional silencing, yet the mechanisms governing the catalytic activation in chromatin context-dependent manner remain unclear. Here we present the cryo-electron microscopy structure of Rpd3L bound to both mono- and di-nucleosome substrate at near-atomic resolution, uncovering a substrate-guided allosteric activation mechanism. Rpd3L adopts an asymmetric architecture, in which the proximal catalytic module anchors the first nucleosome, while the Sin3 PAH domains engage linker DNA to reposition a second nucleosome. This spatial configuration brings the distal catalytic module into proximity with chromatin and unlocks its latent deacetylase activity. Biochemical and mass spectrometry analyses confirm that dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity. Together, these findings establish a hierarchical mechanism by which Rpd3L interprets histone modifications and nucleosome organization to modulate its enzymatic output at promoter regions. Our study provides a framework for understanding higher-order chromatin repression mechanisms by chromatin-regulation complexes and co-repressors.
External linksNucleic Acids Res / PubMed:42152683 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.4 Å
Structure data

64741

9v2v

EMDB-64741, PDB-9v2v:
Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome
Method: EM (single particle) / Resolution: 3.0 Å

64742

9v2w

EMDB-64742, PDB-9v2w:
Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae s288c (yeast)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
  • Saccharomyces cerevisiae (strain S288C) (yeast)
KeywordsGENE REGULATION/DNA / Histone deacetylase complex / Histone modification / Rpd3L / Cryo-EM / mono-nucleosome / GENE REGULATION-DNA complex / di-nucleosome

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