SIR3

Summary: IBA-seeded from phylogenetic inference. SIR3 directly localizes to euchromatic origins but suppresses MCM loading (negative regulation), not initiation.

Reason: SIR3 does not participate in DNA replication initiation. SIR3 suppresses MCM loading and origin activity (GO:0008156), which is negative regulation, not initiation itself. Core machinery includes ORC, CDC6, CDT1, MCM2-7, not SIR3.

Summary: IBA annotation. SIR3 binds nucleosomes at origins, not origins themselves. Origins are DNA sequences recognized by ORC.

Reason: SIR3 binds chromatin/nucleosomes near origins, not the origin DNA itself. Origin binding is attributed to ORC (origin recognition complex). This confuses SIR3 nucleosome binding with origin recognition.

Summary: IBA annotation with no supporting evidence. SIR3 has no known role in checkpoint signaling.

Reason: SIR3 functions in heterochromatin formation and chromatin structure, not DNA damage or replication checkpoints. This is a spurious IBA inference.

Summary: SIR3 directly binds DNA. Experimentally validated with both ds and ssDNA binding (PMID:19099415). More specific molecular functions exist (GO:0003690, GO:0003697) but DNA binding is also appropriate.

Reason: SIR3 is experimentally shown to bind both double-stranded (PMID:19099415) and single-stranded DNA (PMID:19099415). This is a core molecular function supporting its role in chromatin structure and transcriptional regulation.

Summary: Critical molecular function. SIR3 binds chromatin and nucleosomes (PMID:19217406, PMID:18195043). Direct experimental evidence with IDA code also available (PMID:18195043).

Reason: SIR3 directly binds to chromatin and nucleosomes, which is central to its function in heterochromatin formation. This is a core molecular mechanism.

Summary: SIR3 localizes to the nucleus where it functions in heterochromatin formation at mating-type loci, telomeres, and euchromatic origins.

Reason: SIR3 is exclusively nuclear, functioning at HML, HMR, telomeres, rDNA, and euchromatic origins. Correct cellular localization annotation.

Summary: SIR3 is a chromosomal protein functioning at multiple chromosomal loci.

Reason: SIR3 localizes to chromosomes including telomeres, mating-type loci, rDNA, and euchromatic origins. Correct annotation.

Summary: SIR3 is not involved in the transcription process itself. SIR3s role is in transcriptional repression through heterochromatin formation (GO:0006354 or GO:0030466 are more accurate).

Reason: GO:0006351 refers to the core transcription machinery. SIR3 is not involved in RNA synthesis. Instead, SIR3 negatively regulates transcription by forming repressive heterochromatin. More specific and accurate terms are GO:0006354 (negative regulation) or GO:0030466 (mating-type silencing).

Proposed replacements: negative regulation of transcription, DNA-templated silent mating-type cassette heterochromatin formation

Summary: SIR3 binds RAP1 protein (PMID:11689698). However, protein binding is too vague - more specific binding terms exist.

Reason: GO:0005515 (protein binding) is uninformative per curation guidelines. SIR3 binds specific partners (SIR2, SIR4, RAP1, histones). These are better captured by identical protein binding (GO:0042802), nucleosome binding (GO:0031491), and chromatin binding (GO:0003682).

Summary: Protein complex membership by mass spectrometry. Too vague compared to specific binding partners and complex membership annotations.

Reason: Generic protein binding obscures the specific complex and binding partners documented in this study.

Summary: Protein complex annotation. Vague annotation.

Reason: Generic protein binding is less informative than specific binding partner and complex annotations.

Summary: SIR3 domain structure and interactions (PMID:16717101). SIR3 binding to SIR4 and other partners. Generic term.

Reason: Uninformative without specifying the actual binding partners and interactions.

Summary: RAP1 binding. Generic annotation.

Reason: Protein binding is too vague. The specific RAP1 interaction should be documented elsewhere.

Summary: SIR3 forms homodimers through nested deletion and biochemical analysis (PMID:16717101). Essential structural feature.

Reason: SIR3 self-associates to form oligomers and homodimers. This is a core structural feature essential for heterochromatin formation. Directly supports GO:0005677 complex formation.

Summary: SIR3 homodimer formation confirmed by chromatin-associated interactome mapping (PMID:21179020).

Reason: Multiple independent experimental approaches confirm SIR3 homodimerization is essential for function.

Summary: SIR3 C-terminal winged helix domain mediates homodimerization, essential for heterochromatin formation (PMID:23299941).

Reason: Structural evidence shows SIR3 WH domain dimerizes and this is required for silencing. Core structural function.

Summary: SIR3 is essential for heterochromatin formation. Core function documented in budding yeast silencing complexes review.

Reason: SIR3 is a core component of the Sir2-3-4 complex required for heterochromatin formation at mating-type loci, telomeres, and rDNA. This is the defining function of SIR3.

Summary: Direct experimental evidence of nucleic acid binding through domain organization and biochemical characterization (PMID:17176117).

Reason: EXP evidence from biochemical studies. SIR3 directly binds nucleic acids. Experimentally validated.

Summary: SIR3 localizes to origin-adjacent nucleosomes but does not bind origins themselves. Origins are DNA sequences bound by ORC.

Reason: SIR3 binds nucleosomes that are located near origins (PMID:29795547), not the origin DNA itself. The origin DNA is recognized and bound by ORC (origin recognition complex). This annotation confuses nucleosome binding with origin binding.

Summary: SIR3 is an integral component of the chromatin silencing complex (Sir2-SIR3-SIR4). Both is_active_in and part_of relations exist in GOA.

Reason: SIR3 is a core structural component of the Sir2-3-4 silent chromatin complex documented by co-immunoprecipitation and biochemical studies.

Summary: SIR3 suppresses MCM loading at euchromatic origins and maintains repression at heterochromatic origins. Core negative regulatory function.

Reason: SIR3 directly suppresses MCM complex loading at the majority of euchromatic origins and negatively regulates rDNA and telomeric origin function. This is a key SIR3 function distinguishing it from initiation role.

Summary: SIR3 is required for silencing at telomeres and subtelomeric regions. Classic position-effect data.

Reason: SIR3 is essential for telomeric and subtelomeric heterochromatin. Core function of SIR complex.

Summary: SIR3 role in telomeric silencing in context of lifespan and aging.

Reason: Multiple genetic studies confirm SIR3 requirement for telomeric silencing and its connection to aging phenotypes.

Summary: SIR3 mutation effects on telomeric silencing and NHEJ processes.

Reason: SIR3 is required for telomeric silencing and maintenance.

Summary: SIR3 localizes to telomeric regions and is required for telomere clustering in quiescent cells.

Reason: SIR3 directly localizes to and functions at telomeres. Documented localization via ChIP.

Summary: Direct experimental evidence of SIR3 binding at telomeres by ChIP.

Reason: ChIP evidence documenting SIR3 at telomeric chromatin.

Summary: SIR3 is a component of heterochromatin. Required for formation and maintenance.

Reason: SIR3 localizes to and is integral part of heterochromatin at all silenced loci.

Summary: HDA from mitochondrial proteomics study. SIR3 is not mitochondrial.

Reason: SIR3 is a nuclear protein with no known mitochondrial function or localization. HDA from mitochondrial proteomics is a false positive, likely from contamination in the MS sample.

Summary: HDA from mitochondrial proteomics. Spurious annotation.

Reason: SIR3 is exclusively nuclear. This HDA is likely experimental artifact.

Summary: sir3 mutants are genuinely NHEJ-defective, but the defect is an indirect consequence of losing HML/HMR silencing - derepressed a1/alpha2 shuts off the NHEJ factor NEJ1 - rather than a direct role for SIR3 in end-joining, so a regulation term describes the biology better than the participant term.

Reason: The IMP evidence is real and the cited paper assayed SIR3 directly: "using an in vivo plasmid rejoining assay, we demonstrate that SIR2, SIR3 and SIR4...are essential for Ku-dependent DSB repair" (PMID:9501103), so the previous REMOVE contradicted its own cited source. The mechanism, however, is indirect, and that determines the correct term. Lee et al. found that "the effect of deleting SIR genes is largely attributable to derepression of silent mating-type genes" (PMID:10421582), and Kegel et al. identified the target: NEJ1 is haploid-specific, its promoter carries a consensus a1/alpha2 repressor site, and its transcription is completely repressed in sir haploids - so loss of SIR silencing lets a1/alpha2 shut NEJ1 off (PMID:11676923). Decisively, constitutive Nej1p expression "completely rescued the defect in NHEJ, thus showing that Sir proteins per se were dispensable for NHEJ" (PMID:11676923). SIR3 is thus not part of the core NHEJ machinery (Ku70/80, Lig4/Dnl4, Xrs2) and, on the rescue evidence, is not a participant in end-joining at all; it acts upstream by silencing HML/HMR so that NEJ1 stays expressed. (Lee et al. do report a residual "minor role" for Sir proteins in end-joining, but the Kegel rescue shows it is not required.) The general regulation term GO:2001032 is proposed rather than the directional GO:2001034 because SIR3 acts permissively - maintaining NEJ1 expression - rather than actively modulating repair. NOTE: the identical GO:0006303/IMP/PMID:9501103 annotation is currently adjudicated differently on SIR2 (REMOVE) and SIR4 (MARK_AS_OVER_ANNOTATED) even though a single experiment assayed all three; those entries should be reconciled with this rationale in a separate pass.

Proposed replacements: regulation of double-strand break repair via nonhomologous end joining

Summary: Classic position-effect data. SIR3 is essential for HML and HMR silencing. Founding function of the SIR genes.

Reason: SIR3 is required for mating-type silencing at HML and HMR loci. This is a core function defined in the original SIR studies.

Summary: SIR3 is part of the Sir complex that localizes to telomeres. Ku complex recruitment involves SIR4.

Reason: SIR3 as part of the Sir complex is required for complex localization to telomeres for telomerase recruitment and telomere maintenance.

Summary: SIR3 participates in telomere clustering and nuclear organization.

Reason: SIR3 as component of Sir complex participates in telomere tethering and clustering at nuclear periphery.

Summary: SIR3 required for telomere hyperclustering and nuclear organization in quiescent cells.

Reason: Additional evidence for SIR3s role in telomere organization.

Summary: SIR3 localization at telomeres documented.

Reason: Confirms telomeric localization of SIR3 at functional loci.

Summary: Long-range communication and chromatin structure study. SIR3 directly binds chromatin.

Reason: Experimental evidence for chromatin binding in HMR silencer analysis.

Summary: SIR3 binds double-stranded DNA in vitro. Direct biochemical evidence.

Reason: SIR3 directly binds dsDNA. Core molecular function.

Summary: SIR3 binds single-stranded DNA in vitro. Direct biochemical evidence.

Reason: SIR3 binds both ss and dsDNA. Core molecular function.

Summary: SIR3 redistributes from telomeres to nucleolus in long-lived yeast strains. Reflects differential regulation in aging.

Reason: SIR3 can localize to nucleolus where rDNA silencing occurs. Secondary but documented localization site. Important for aging phenotypes.

Summary: SIR3 BAH domain structure and function essential for HM silencing.

Reason: Structural basis of SIR3 function in mating-type silencing documented.

Summary: Genetic interaction studies showing SIR3-SIR1 relationship in silencing.

Reason: Genetic interactions confirm SIR3s role in mating-type silencing.

Summary: SIR3 binds nucleosomes in vitro. Histone H4 tail and H3K79 are contact sites. Core mechanism of action.

Reason: SIR3 directly binds nucleosomes through multiple histone contact sites. Core mechanism. Biochemically validated.

Summary: SIR3 C-terminal domain involvement in heterochromatin initiation and spreading.

Reason: Functional analysis of SIR3 domains in heterochromatin formation and maintenance.

Summary: SIR3 was recovered as an IMP hit in a genome-wide deletion screen for suppressors of a nonstop-mRNA reporter. The full text (now cached) does not name or discuss SIR3 anywhere in its body/discussion text, and the results table listing all 15 tightly-linked genes with their individual phenotype values is not extractable from the cached page, so SIR3's specific data (magnitude of effect, mechanism) could not be verified.

Reason: Per project guidance, an experimental (IMP) annotation should not be REMOVEd just because the curator cannot confirm the supporting detail from an abstract-only or partially-recovered full text - that is exactly the situation here (full text was fetched but the specific results table entry for SIR3 is not present in the extracted text, and SIR3 is not named in the surrounding prose). The original REMOVE action asserted a specific mechanistic judgment ("indirect through secondary effects on gene expression or cell stress responses") that is not supported by anything actually verifiable in the cached source. Marking UNDECIDED rather than REMOVE or ACCEPT until the primary data for this specific annotation can be confirmed. The concrete unblocker is Table 2 of PMID:17660569 (or the underlying SGD annotation detail), which lists the per-gene phenotype values for the 15 linked genes but was not recovered by full-text extraction; whoever revisits this should start there.