SIR3 chromatin-silencing protein SIR3 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: SIR3
Official Full Name: chromatin-silencing protein SIR3
Primary source: SGD:S000004434
Locus tag: YLR442C
See related: AllianceGenome:SGD:S000004434; FungiDB:YLR442C; VEuPathDB:YLR442C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: CMT1; MAR2; STE8
Summary: Enables DNA replication origin binding activity; nucleosome binding activity; and single-stranded DNA binding activity. Involved in several processes, including double-strand break repair via nonhomologous end joining; establishment of protein-containing complex localization to telomere; and negative regulation of macromolecule metabolic process. Located in chromosome, telomeric region; heterochromatin; and nucleolus. Part of chromatin silencing complex. Human ortholog(s) of this gene implicated in Meier-Gorlin syndrome 1. Orthologous to human ORC1 (origin recognition complex subunit 1). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See SIR3 in Genome Data Viewer

Location:: chromosome: XII

Exon count:: 1

Sequence:: Chromosome: XII; NC_001144.5 (1019315..1022251, complement)

Chromosome XII - NC_001144.5 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001144.5

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae.
Title: Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae.
Sir3 mediates long-range chromosome interactions in budding yeast.
Title: Sir3 mediates long-range chromosome interactions in budding yeast.
Direct interaction of Sir3 with O-acetyl-ADP-ribose promotes the further spreading of Sir3 along telomeres.
Title: The Capability of O-Acetyl-ADP-Ribose, an Epigenetic Metabolic Small Molecule, on Promoting the Further Spreading of Sir3 along the Telomeric Chromatin.
Yeast Sir2 and Sir3 heterochromatin proteins directly modify the local chromatin environment of euchromatic DNA replication origins.
Title: Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins.
Here, the authors analyze binding of the Sir proteins to reconstituted mono-, di-, tri-, and tetra-nucleosomal chromatin templates and show that key Sir-Sir interactions bridge only sites on different nucleosomes but not sites on the same nucleosome, and are therefore 'interrupted' with respect to sites on the same nucleosome.
Title: Heterochromatin assembly by interrupted Sir3 bridges across neighboring nucleosomes.
Repair of UV-induced DNA lesions in Saccharomyces cerevisiae telomeres is moderated by Sir2 and Sir3, and inhibited by yKu-Sir4 interaction.
Title: Repair of UV-induced DNA lesions in natural Saccharomyces cerevisiae telomeres is moderated by Sir2 and Sir3, and inhibited by yKu-Sir4 interaction.
silencing requires Sir2, a highly-conserved NAD(+)-dependent histone deacetylase. At locations other than the rDNA, silencing also requires additional Sir proteins, Sir1, Sir3, and Sir4 that together form a repressive heterochromatin-like structure termed silent chromatin.
Title: The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae.
results suggest that Sir3 exhibits novel binding parameters and gene regulatory functions at the CN binding domains.
Title: Analysis of novel Sir3 binding regions in Saccharomyces cerevisiae.
Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome. We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres.
Title: Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres.
Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme.
Title: Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA replication origin binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA replication origin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleosome binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA replication initiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of protein-containing complex localization to telomere	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic DNA replication checkpoint signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, non-stop decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in silent mating-type cassette heterochromatin formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in silent mating-type cassette heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in subtelomeric heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere tethering at nuclear periphery	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin silencing complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	IMP Inferred from Mutant Phenotype more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	HDA more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chromatin-silencing protein SIR3

NP_013547.3

Silencing protein; interacts with Sir2p, Sir4p, and histone H3/H4 tails to establish transcriptionally silent chromatin; required for spreading of silenced chromatin; recruited to chromatin through interaction with Rap1p; C-terminus assumes variant winged helix-turn-helix (wH) fold that mediates homodimerization, which is critical for holo-SIR complex loading; required for telomere hypercluster formation in quiescent yeast cells; has paralog ORC1 from whole genome duplication

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001144.5 Reference assembly

Range

1019315..1022251 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182330.3 → NP_013547.3 TPA: chromatin-silencing protein SIR3 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013547.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VZ77, E9P924, P06701

UniProtKB/TrEMBL

B3RHV1, C8ZE50, G2WJQ3, N1NZY0

Conserved Domains (2) summary

COG1474
Location:528 → 962

CDC6; Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair]

cd04720
Location:5 → 189

BAH_Orc1p_Yeast; BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a ...