SIR4 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: SIR4
Primary source: SGD:S000002635
Locus tag: YDR227W
See related: AllianceGenome:SGD:S000002635; FungiDB:YDR227W; VEuPathDB:YDR227W
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: ASD1; STE9; UTH2
Summary: Enables double-stranded DNA binding activity; molecular adaptor activity; and nucleosome binding activity. Involved in several processes, including double-strand break repair via nonhomologous end joining; establishment of protein-containing complex localization to telomere; and heterochromatin assembly. Located in chromosome, telomeric region. Part of chromatin silencing complex. [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (917571..921647)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid.
Title: SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid.
Esc1-interacting region of Sir4 is Dbf4-related H-BRCT domain
Title: Discovery and Evolution of New Domains in Yeast Heterochromatin Factor Sir4 and Its Partner Esc1.
A direct interaction between Ubp10 and the Sir2/4 sub-complex facilitates Ubp10 recruitment to chromatin via a co-assembly mechanism.
Title: Recruitment and allosteric stimulation of a histone-deubiquitinating enzyme during heterochromatin assembly.
the silencing factor Sir4, NE-associated Esc1, the SUMO E3 ligase Siz2, and the nuclear pore complex (NPC) protein Nup170-physically and functionally interact with one another and a subset of NPC components (nucleoporins or Nups).
Title: Yeast silencing factor Sir4 and a subset of nucleoporins form a complex distinct from nuclear pore complexes.
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.
nse3-1/ sir4 Delta double mutants show additive defects for telomere shortening and TPE indicating the contribution of Smc5/6 to telomere homeostasis is only in partial overlap with SIR factor silencing. These findings support a role for Smc5/6 in telomere maintenance that is separate from its canonical role(s) in HR-mediated events during replication and telomere elongation.
Title: Smc5/6 Is a Telomere-Associated Complex that Regulates Sir4 Binding and TPE.
data support a model whereby the demethylation of histone H3 K79 and changes in Sir4 abundance and availability define two rate-limiting steps that regulate de novo assembly of heterochromatin
Title: Competition between Heterochromatic Loci Allows the Abundance of the Silencing Protein, Sir4, to Regulate de novo Assembly of Heterochromatin.
The authors show that Sir4 - a previously identified Ku-binding protein that is a component of telomeric silent chromatin - is required for Ku-mediated telomere lengthening and telomerase recruitment.
Title: The Ku subunit of telomerase binds Sir4 to recruit telomerase to lengthen telomeres in S. cerevisiae.
These results demonstrate that the SCF(Dia2) complex is involved in transcriptional silencing, ubiquitylates Sir4, and regulates transcriptional silencing during the cell cycle.
Title: The SCFDia2 ubiquitin E3 ligase ubiquitylates Sir4 and functions in transcriptional silencing.

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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 double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables molecular adaptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables nucleosome binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
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 positive regulation of heterochromatin formation	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, 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 nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chromatin-silencing protein SIR4

NP_010513.1

SIR protein involved in assembly of silent chromatin domains; silent information regulator (SIR) along with SIR2 and SIR3; involved in assembly of silent chromatin domains at telomeres and the silent mating-type loci; some SIR4 alleles prolong lifespan; required for Ku-mediated telomerase recruitment, telomere lengthening, and telomere hypercluster formation in quiescent yeast cells

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_001136.10 Reference assembly

Range

917571..921647

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180535.1 → NP_010513.1 TPA: chromatin-silencing protein SIR4 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010513.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VSK9, P11978

UniProtKB/TrEMBL

A6ZYI1, B3LG60, N1P8F6

Conserved Domains (2) summary

PTZ00449
Location:2 → 106

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

cd13746
Location:801 → 893

Sir4p-SID_like; The SID domain of Saccharomyces cerevisiae silent information regulator 4, a Sir2p interaction domain; and related domains