| Category | Evidence-backed details | Key citations (with year) | URL |
|---|---|---|---|
| Verified identity | **RCO1/YMR075W/UniProt Q04779** in *Saccharomyces cerevisiae* is the **Rco1** subunit of the **Rpd3S histone deacetylase complex**; primary literature describes it as a **PHD zinc-finger/plant homeodomain-containing** chromatin regulator, not an enzyme on its own. | Li 2023 (pqac-00000005, pqac-00000045); Ruan 2016 (pqac-00000003, pqac-00000006) | https://doi.org/10.1038/s41594-023-01121-5; https://doi.org/10.1074/jbc.m115.703637 |
| Molecular function within Rpd3S | Rco1 helps target and activate **Rpd3S** on transcribed chromatin so the complex can **deacetylate histones in coding regions after Pol II passage**, maintaining hypoacetylated gene bodies and **suppressing cryptic intragenic transcription**. It acts together with Eaf3, Sin3, Rpd3, and Ume1. | Drouin 2010 (pqac-00000008); Govind 2010 (pqac-00000009); Li 2023 (pqac-00000005) | https://doi.org/10.1371/journal.pgen.1001173; https://doi.org/10.1016/j.molcel.2010.07.003; https://doi.org/10.1038/s41594-023-01121-5 |
| Domains / reader activities | Rco1 contains **two PHD fingers (PHD1, PHD2)**. These domains bind the **extreme H3 N-terminus (H3 1–20)** and preferentially read **unmodified H3K4 (H3K4me0)**; **H3K4me3 reduces binding**, helping exclude Rpd3S from promoter chromatin. Rco1 also contains a **SID/MRG-interacting region** that connects functionally to Eaf3. | McDaniel 2016 (pqac-00000012, pqac-00000016, pqac-00000017); Guan 2023 (pqac-00000019); Zhang 2023 (pqac-00000027) | https://doi.org/10.1074/jbc.m116.720193; https://doi.org/10.1038/s41586-023-06349-1; https://doi.org/10.1038/s41422-023-00884-2 |
| Binding partners / complex architecture | Core partners are **Rpd3, Sin3, Ume1, and Eaf3**. Structural studies show **two copies of Rco1 and two copies of Eaf3** organized around catalytic Rpd3; Rco1 forms **Eaf3–Rco1 heterodimers** and can homodimerize, making it a major interaction hub in Rpd3S. | Markert 2023 (pqac-00000024, pqac-00000053); Li 2023 (pqac-00000026); Ruan 2016 (pqac-00000003, pqac-00000014) | https://doi.org/10.1038/s41467-023-43968-8; https://doi.org/10.1038/s41594-023-01121-5; https://doi.org/10.1074/jbc.m115.703637 |
| Recruitment determinants | Recruitment/function is coupled to **Set2-dependent H3K36 methylation** via **Eaf3 chromodomain** recognition, while Rco1 contributes **H3 tail readout** and nucleosome engagement. Rpd3S recruitment to active ORFs is also coordinated by **RNAPII CTD phosphorylation (especially Ser5P, with S2P contribution)** and **DSIF/Spt4-Spt5**. Recent work further suggests an **Rco1 IDR** contributes to **Pol II CTD association**. | Drouin 2010 (pqac-00000008, pqac-00000034); Govind 2010 (pqac-00000009); Li 2024 preprint (pqac-00000044) | https://doi.org/10.1371/journal.pgen.1001173; https://doi.org/10.1016/j.molcel.2010.07.003; https://doi.org/10.21203/rs.3.rs-4000909/v1 |
| Cellular localization | Rco1 is predominantly **chromatin-associated** and localizes to **active ORFs / gene bodies** rather than promoters, consistent with Rpd3S function in transcribed coding regions. Fractionation studies place wild-type Rco1 mainly in the **chromatin fraction**. | Drouin 2010 (pqac-00000008); McDaniel 2016 (pqac-00000012); McDaniel thesis 2016 (pqac-00000013) | https://doi.org/10.1371/journal.pgen.1001173; https://doi.org/10.1074/jbc.m116.720193; https://doi.org/10.17615/shj3-8048 |
| Mechanistic insight from 2023–2024 studies | 2023 cryo-EM studies show **multivalent nucleosome engagement**: Rco1, Eaf3, and Sin3 contact **H3K36me3-marked nucleosomes, nucleosomal DNA, and linker DNA**. Rco1 PHD1 helps place the H3 tail toward the catalytic center, while alternate engagement modes explain context-dependent H3/H4 deacetylation. A 2024 commentary interprets Rco1 as a **specificity determinant** for gene-body chromatin and lysine selection. | Guan 2023 (pqac-00000030, pqac-00000040); Li 2023 (pqac-00000026); Carrozza & Workman 2024 (pqac-00000043) | https://doi.org/10.1038/s41586-023-06349-1; https://doi.org/10.1038/s41594-023-01121-5; https://doi.org/10.1038/s41422-023-00899-9 |
| Phenotypes / functional readouts | **rco1Δ** or **PHD-disrupting mutants** impair nucleosome/chromatin binding and cause **cryptic transcription** phenotypes in reporter assays; truncations or mutations in key Rco1 regions compromise Rpd3S function even when complex assembly is retained. Genetic studies also show Rco1-mediated Rpd3S is antagonized by **H3K4 methylation** and promoted by **H3K36 methylation**. | Ruan 2016 (pqac-00000011); McDaniel 2016 (pqac-00000012, pqac-00000018); Lee 2018 (pqac-00000010) | https://doi.org/10.1074/jbc.m115.703637; https://doi.org/10.1074/jbc.m116.720193; https://doi.org/10.1534/g3.118.200589 |
| Key quantitative metrics | Reported values include **~410 kDa** for Rpd3S, **2× Rco1 + 2× Eaf3** stoichiometry in 2023 structures, and cryo-EM resolutions of **2.8 Å** (Markert 2023), **3.1/3.0 Å** with **10.5 Å** di-nucleosome map (Li 2023), and **3.5 Å** (Dong 2023). Rpd3S shows a **modest preference for 30–40 bp linker DNA** and di-nucleosomes. One measured affinity from structural/biochemical work: **Rco1 PHD1 binds H3(1–10) with Kd ~39 µM**; PHD2 showed no detectable H3(1–10) reader activity in that assay. | Markert 2023 (pqac-00000053); Li 2023 (pqac-00000050); Dong 2023 (pqac-00000054); Ruan 2016 (pqac-00000052); Li/Guan preprint 2023 (pqac-00000049) | https://doi.org/10.1038/s41467-023-43968-8; https://doi.org/10.1038/s41594-023-01121-5; https://doi.org/10.1038/s41422-023-00869-1; https://doi.org/10.1074/jbc.m115.703637; https://doi.org/10.21203/rs.3.rs-2060494/v1 |
| Enzymatic/substrate specificity context | Rco1 is **not the catalytic HDAC**; it is a **reader/targeting and regulatory subunit**. Recent structural commentary notes Rpd3S deacetylates **H3K23 and H3K14 more efficiently than H3K9, H3K18, and H3K27**, and some structures place **H3K18** or H3/H4 tails near the active site depending on nucleosome engagement mode. | Carrozza & Workman 2024 (pqac-00000047); Guan 2023 (pqac-00000019, pqac-00000025) | https://doi.org/10.1038/s41422-023-00899-9; https://doi.org/10.1038/s41586-023-06349-1 |


*Table: This table compiles evidence-backed functional annotation for Saccharomyces cerevisiae RCO1/Q04779, emphasizing its role as the PHD-containing targeting subunit of the Rpd3S histone deacetylase complex. It combines recent 2023-2024 structural advances with foundational mechanistic studies and includes URLs for rapid source checking.*