Structure of histone deacetylase complex Rpd3S bound to nucleosome
Structure of histone deacetylase complex Rpd3S bound to nucleosome is a research paper published in Nature Structural & Molecular Biology (2023). On theSindex it has a DataRank of 0.660. It has been cited 17 times, with 17 citing works in its 1-hop citation network.
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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FAIR Checklist
Context only (not used in score)- Has DOI
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
DataRank Breakdown
Base Score Contribution
0.434
From this paper's citation signal
Citation Network Contribution
0.227
From 13 citing papers with measurable signal
Top 5 citers driving the network score
Ranked by citation count — the same ordering the engine uses when summing log1p(Cq) over citers.
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- Chromatin Modifications and Their FunctionCell200710,704 citationsDataRank 1.4
Why this DataRank?
DataRank blends this paper's own citation count with the influence of the papers that cite it. Here, roughly 66% comes from its base citations and 34% from the citation network (13 citing papers contributed measurable signal).
- Base score B(p)
- log1p(citation_count) — grows sub-linearly, so a paper with 1,000 citations is not 10× a paper with 100.
- Network N(p)
- Σ over citers of log1p(Cq) ÷ max(outdegreeq, 1). Being cited by a highly-cited paper with few references counts most.
- Damping factor d = 0.85
- DataRank = (1−d)·B(p) + d·N(p) — the two cards above are each already multiplied by their share.
- Self-citations excluded
- Citers sharing any OpenAlex author ID with this paper are filtered out before the network sum.
Citers are pulled from OpenAlex sorted by cited_by_count:descand capped per paper, so when the cap binds we keep the highest-signal references and the score is reproducible across reruns.
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