Gene Ontology annotation through association of InterPro records with GO terms
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
Electronic Gene Ontology annotations created by ARBA machine learning models
Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae.
Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae.
Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3.
Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisiae.
Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing.
Sir proteins, Rif proteins, and Cdc13p bind Saccharomyces telomeres in vivo.
Role of yeast SIR genes and mating type in directing DNA double-strand breaks to homologous and non-homologous repair paths.
Nej1p, a cell type-specific regulator of nonhomologous end joining in yeast.
Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast.
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
The proteome of Saccharomyces cerevisiae mitochondria.
Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions.
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Structure and function of the Saccharomyces cerevisiae Sir3 BAH domain.
Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments.
Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.
Sir3 C-terminal domain involvement in the initiation and spreading of heterochromatin.
The nuclear GTPase Gsp1p can affect proper telomeric function through the Sir4 protein in Saccharomyces cerevisiae.
Domain organization and quaternary structure of the Saccharomyces cerevisiae silent information regulator 3 protein, Sir3p.
A genomic screen in yeast reveals novel aspects of nonstop mRNA metabolism.
Long-range communication between the silencers of HMR.
Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.
Reconstitution of yeast silent chromatin multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro.
An auxiliary silencer and a boundary element maintain high levels of silencing proteins at HMR in Saccharomyces cerevisiae.
Defining the budding yeast chromatin-associated interactome.
A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms.
Dimerization of Sir3 via its C-terminal winged helix domain is essential for yeast heterochromatin formation.
The Ku subunit of telomerase binds Sir4 to recruit telomerase to lengthen telomeres in S. cerevisiae.
Spatial reorganization of telomeres in long-lived quiescent cells.
Quiescent Saccharomyces cerevisiae forms telomere hyperclusters at the nuclear membrane vicinity through a multifaceted mechanism involving Esc1, the Sir complex, and chromatin condensation.
Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins.
Reciprocal interactions between mtDNA and lifespan control in budding yeast.
Falcon deep research report on SIR3
-
Sir3 is the principal nucleosome-binding/structural subunit of the
Sir2/3/4 silencing complex. It binds chromatin via its conserved
N-terminal BAH domain and oligomerizes and participates in
spreading/compaction through additional conserved regions, including a
C-terminal AAA-like domain that lacks canonical ATPase activity.
"Across classic biochemistry and structural work, **Sir3 is the principal nucleosome-binding/structural subunit** of the Sir2/3/4 complex. It binds chromatin via its conserved **N-terminal BAH (bromo-adjacent homology) domain**, and it oligomerizes and participates in spreading/compaction through additional conserved regions, including a **C-terminal AAA-like domain** (lacking canonical ATPase activity).
"
-
The Sir3 BAH domain is a histone-modification-sensitive nucleosome
reader; its association with nucleosomes is impaired by H4K16
acetylation and H3K79 methylation.
"**BAH domain as a nucleosome reader.** Sir3 contains an N-terminal BAH domain that directly binds nucleosomes and is **sensitive to histone modification state**, a key aspect of how silent chromatin is specified.
"
-
A 3.0 Angstrom crystal structure of the Sir3 BAH domain bound to the
nucleosome shows two Sir3 BAH domains binding one nucleosome (one per
face) making extensive contacts primarily with the core histones
(notably the H4 N-terminal tail and the H3/H4 LRS surface) rather than
DNA, implicating H4K16 and H3K79.
"A landmark structure solved a **3.0 Å crystal structure** of the Sir3 **BAH domain bound to the nucleosome**, showing that Sir3 BAH forms extensive contacts primarily with **histones (not DNA)**, including the **H4 N-terminal tail** and the H3/H4 LRS surface; critically, the structure orders and implicates residues such as **H4K16** and **H3K79**, whose modification state regulates silencing.
"
-
Read-write spreading logic: Sir2 deacetylates histone H4K16 to create
binding-competent nucleosomes; Sir3 preferentially recognizes
deacetylated H4K16 nucleosomes; Sir3 dimers linked through Sir4 dimers
support cooperative binding to paired nucleosomes and cis-spreading of
the silent domain from silencers.
"A widely used mechanistic model is an iterative “read–write” logic in which **Sir2 deacetylates histone H4K16**, creating binding-competent nucleosomes; **Sir3 preferentially recognizes deacetylated H4K16 nucleosomes** and, together with Sir4-mediated assemblies, supports cooperative binding and **cis-spreading** of the silent domain outward from silencers.
"
-
Sir3 functions in the nucleus on chromatin, with classical sites of
action at HML/HMR and telomere-proximal/subtelomeric regions, where it
binds nucleosomes as part of the Sir2/3/4 silencing machinery.
"Sir3 functions in the **nucleus** on **chromatin**, with classical sites of action at **HML/HMR** and **telomere-proximal/subtelomeric regions**, where it binds nucleosomes as part of the Sir2/3/4 silencing machinery
"
-
Beyond canonical silent domains, Sir3 also makes transient direct
contacts with euchromatin at large scale; Nanopore-MetID identified
1,197 genes (~19% of genes) as Sir3 contact targets, with high-density
occupancy concentrated about +/-2 kb around subtelomeric nucleation
sites.
"Recent mapping adds that Sir3 also makes **transient direct contacts with euchromatin** at large scale, beyond canonical silent domains.
"
-
Sir3 chromatin contacts depend on the Sir2/3/4 complex: subtelomeric
Sir3 methylation is abolished in sir2-delta cells and reduced about
2-fold in sir4-delta cells.
"Subtelomeric Sir3 methylation is abolished in *sir2Δ* and reduced about 2-fold in *sir4Δ*, consistent with Sir3 acting within the Sir2/3/4 complex
"