Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Global analysis of protein localization in budding yeast.
Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone.
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription.
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.
Proteome survey reveals modularity of the yeast cell machinery.
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors.
Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae.
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
Histone H3K4 and K36 methylation, Chd1 and Rpd3S oppose the functions of Saccharomyces cerevisiae Spt4-Spt5 in transcription.
Defining the budding yeast chromatin-associated interactome.
Nascent transcript sequencing visualizes transcription at nucleotide resolution.
The Rpd3 core complex is a chromatin stabilization module.
The yeast Snt2 protein coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress.
The roles of the catalytic and noncatalytic activities of Rpd3L and Rpd3S in the regulation of gene transcription in yeast.
Eaf5/7/3 form a functionally independent NuA4 submodule linked to RNA polymerase II-coupled nucleosome recycling.
The cellular economy of the Saccharomyces cerevisiae zinc proteome.
The social and structural architecture of the yeast protein interactome.
Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo.
Falcon deep research report on RCO1 (Q04779, YMR075W)
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RCO1 (Q04779/YMR075W) encodes Rco1, a non-catalytic PHD zinc-finger chromatin
regulatory protein that is a unique, defining subunit of the Rpd3S histone
deacetylase complex. It is not itself a deacetylase but acts as a reader,
targeting, and regulatory subunit required for Rpd3S activity and chromatin
engagement at gene bodies.
"**RCO1 encodes Rco1, a non-catalytic chromatin regulatory protein**. It is not itself a histone deacetylase; rather, it is a **reader/targeting and regulatory subunit** required for proper activity and chromatin engagement of the **Rpd3S (Rpd3 small) HDAC complex**."
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Rco1 contains two plant homeodomain (PHD) zinc-finger modules (PHD1 and PHD2)
that bind the extreme N-terminus of histone H3 (H3 1-20). H3K4 trimethylation
reduces this binding, providing a mechanism that restricts Rpd3S away from
H3K4me3-rich promoter nucleosomes. The PHD fingers thus read unmodified H3K4
(H3K4me0).
"Rco1 contains **two plant homeodomain (PHD) zinc-finger modules (PHD1 and PHD2)**. Biochemical evidence indicates that both PHD1 and PHD2 bind the **extreme N-terminus of histone H3 (H3 1–20)** and that **H3K4 trimethylation reduces binding**—a mechanism that helps restrict Rpd3S away from promoter nucleosomes enriched in H3K4me3."
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The primary biological role of Rpd3S, dependent on Rco1, is to deacetylate
histones in coding regions in the wake of RNA Pol II, suppressing cryptic
(spurious intragenic) transcription initiation. Recruitment is coupled to the
Set2-dependent H3K36 methylation pathway, read by Eaf3, with Rco1 contributing
complementary histone-tail engagement.
"Rpd3S is a histone deacetylase complex that operates **co-transcriptionally across coding regions (ORFs/gene bodies)** to remove histone acetylation “in the wake” of RNA polymerase II (Pol II), thereby **suppressing cryptic (spurious intragenic) transcription initiation**. Rco1 is one of the Rpd3S-specific subunits underlying this gene-body surveillance function."
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Rco1 is a critical interaction hub within Rpd3S, which is classically a
five-subunit complex (Rpd3, Sin3, Ume1, Eaf3, Rco1). Structural studies show
two copies of Rco1 and two copies of Eaf3 organized around catalytic Rpd3;
the homodimeric Rco1 is required for full function and forms Eaf3-Rco1 modules
via a Sin3 interaction domain (SID) engaging the Eaf3 MRG domain.
"Rpd3S is classically described as a five-subunit complex (Rpd3, Sin3, Ume1, Eaf3, Rco1). Mechanistic work shows Rco1 is a critical interaction hub: Rco1 forms key contacts with Eaf3 (via a Sin3 interaction domain/SID interacting with Eaf3’s MRG domain) and is required for full Rpd3S nucleosome engagement and cryptic transcription suppression."
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Rco1 is predominantly chromatin-associated and localizes to active ORFs/gene
bodies rather than promoters, consistent with the co-transcriptional, gene-body
role of Rpd3S. Fractionation places wild-type Rco1 mainly in the chromatin
fraction.
"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**."
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RCO1/YMR075W/Q04779 is the PHD zinc-finger/plant homeodomain-containing
chromatin regulator subunit of Rpd3S, not an enzyme on its own. The zinc-finger
PHD modules require coordinated zinc for their fold and histone-mark reader
activity.
"**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."