SPT16 is a core subunit of the FACT complex (Facilitates Chromatin Transcription), an essential histone chaperone that reorganizes nucleosomes during transcription, DNA replication, and DNA repair. SPT16 comprises three domains (N-terminal, middle with double PH domains, and C-terminal acidic region) that enable interaction with histones H3/H4 and H2A/H2B dimers, facilitating nucleosome disassembly during polymerase passage and nucleosome reassembly afterward. SPT16 is also known as CDC68 (cell division control protein 68).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006337 nucleosome disassembly | IBA GO_REF:0000033 | ACCEPT | Summary: Nucleosome disassembly is a well-established core function of SPT16/FACT during transcription elongation. IBA (ortholog inference) is appropriate evidence for this deeply characterized function. Reason: SPT16 is a core component of FACT complex that actively facilitates nucleosome disassembly ahead of RNA polymerase II during transcription. The deep research and extensive literature (including Perplexity review citing structural studies showing Spt16 interactions with H3-H4 and H2A-H2B during nucleosome disruption) strongly support this annotation. This is a primary and essential function. Supporting Evidence: file:yeast/SPT16/SPT16-deep-research-perplexity.md See deep research file for comprehensive analysis file:yeast/SPT16/SPT16-deep-research-falcon.md - helps manage nucleosome dynamics (both **disassembly** and **reassembly**) as RNAPII traverses genes, (byrd2024assessingcontributionsof pages 1-2) |
| GO:0032784 regulation of DNA-templated transcription elongation | IBA GO_REF:0000033 | ACCEPT | Summary: Regulation of transcription elongation is a core function of SPT16/FACT. The complex facilitates passage of RNA polymerase II through chromatin by modulating nucleosome structure. Reason: SPT16/FACT is directly involved in promoting transcription elongation by managing nucleosome dynamics. The evidence includes multiple studies showing FACT travels with elongating polymerase II (Mason & Struhl 2003, PMID:14585989) and facilitates fidelity of transcription (evidenced by suppression of cryptic initiation). This is a primary function, not merely a side effect. Supporting Evidence: file:yeast/SPT16/SPT16-deep-research-falcon.md - is required for efficient RNAPII transcription on chromatin templates and functions as a **nucleosome-templated elongation factor**, (schweighofer2025biochemicalinsightsinto pages 22-25, hou2025characterizingthefunctional pages 20-23) |
| GO:0035101 FACT complex | IBA GO_REF:0000033 | ACCEPT | Summary: SPT16 is a core structural component of the FACT complex. This annotation represents membership in the complex with strong phylogenetic support. Reason: SPT16 forms an obligate heterodimeric complex with POB3 (Pob3p) as documented in UniProt and extensively in the literature. IBA evidence from orthologs (SSRP1/SPT16 in other organisms) is appropriate for this structural annotation. Supporting Evidence: file:yeast/SPT16/SPT16-deep-research-falcon.md Spt16 is the large, essential subunit of the conserved yeast FACT histone chaperone complex; in *S. cerevisiae* it forms a heterodimer with Pob3, and budding-yeast FACT function additionally depends on the HMGB protein Nhp6 for efficient nucleosome engagement. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: SPT16 is localized to the nucleus, where it functions in chromatin-associated processes. Reason: Nuclear localization is well-established for SPT16 through multiple studies showing chromatin-association and co-localization with active transcription sites. While IEA is less specific than experimental evidence, nuclear localization is a foundational fact confirmed by direct observation (PMID:10413469). This is a valid cellular component annotation. Supporting Evidence: file:yeast/SPT16/SPT16-deep-research-falcon.md The evidence supports that Spt16 is **nuclear and chromatin-associated**, acting at: |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: SPT16 is localized to chromatin/chromosomes where it functions in nucleosome reorganization during transcription and replication. Reason: SPT16 specifically associates with chromatin and DNA during its biological functions. This is explicitly documented - UniProt states 'Colocalizes with RNA polymerase II on chromatin' and associates with coding regions of histone genes. The annotation is accurate and important for describing where the protein functions. |
| GO:0006260 DNA replication | IEA GO_REF:0000043 | ACCEPT | Summary: SPT16 is involved in DNA replication through its role in nucleosome disassembly ahead of replication forks and histone recycling to daughter strands. Reason: SPT16/FACT is essential for normal replication fork progression. The deep research documents that FACT associates with replication fork components (MCM2-7, Pol alpha) and that SSRP1/SPT16 depletion slows replication forks. The Spt16-N domain interacts with MCM2-7 complex and fork protection complex, enabling parental histone recycling during replication. Supporting Evidence: file:yeast/SPT16/SPT16-deep-research-falcon.md - The Spt16 N-terminal domain binds **Tof1** (fork protection complex) and **MCM2-7** helicase in yeast, linking FACT to fork-associated chromatin transactions. (schweighofer2025biochemicalinsightsintoa pages 22-25, dolson2024impactofthe pages 16-19) - FACT is reported to physically interact with **DNA polymerase Ξ±** in yeast. |
| GO:0006281 DNA repair | IEA GO_REF:0000043 | ACCEPT | Summary: SPT16 participates in DNA repair, particularly base excision repair, through cooperation with chromatin remodelers. Reason: UniProt function section states FACT plays a role in DNA repair. The deep research documentation mentions FACT recruitment to DNA damage sites and cooperation with remodelers to expose damaged DNA for repair (BER pathway). While less extensively characterized than transcription roles, the involvement is documented and scientifically valid. |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000043 | ACCEPT | Summary: SPT16 is fundamentally involved in DNA-templated transcription through its role in nucleosome dynamics during transcription. Reason: SPT16/FACT is a transcription elongation factor essential for efficient transcription through chromatin. This broad annotation captures the core transcriptional role of the protein. IEA from UniProt keyword mapping is appropriate for this well-established function. |
| GO:0006974 DNA damage response | IEA GO_REF:0000043 | ACCEPT | Summary: SPT16 participates in DNA damage response through recruitment to damaged chromatin and cooperation with repair machinery. Reason: UniProt function section mentions DNA repair role and the deep research documents FACT recruitment to DNA damage sites. The involvement in BER and interaction with DNA damage-responsive proteins supports this annotation. |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: While SPT16 does participate in gene expression regulation, this term is very broad and less informative than the specific transcription annotations already present. Reason: This annotation is not incorrect, but it represents a general consequence of SPT16's core transcriptional functions rather than a distinct molecular function. More specific GO terms (transcription elongation, nucleosome disassembly, etc.) better capture SPT16's specific contributions to gene regulation. The annotation should be retained because it is accurate, but marked as non-core. |
| GO:0034728 nucleosome organization | IEA GO_REF:0000117 | ACCEPT | Summary: Nucleosome organization is a core function of SPT16/FACT, encompassing both disassembly and reassembly activities during transcription and replication. Reason: SPT16 directly organizes nucleosomes by controlling their disassembly and reassembly. This is documented throughout literature and is one of the defining functions of the protein. The term appropriately captures the holistic role of nucleosome management. |
| GO:0035101 FACT complex | IEA GO_REF:0000120 | ACCEPT | Summary: This duplicate annotation (same GO term as IBA annotation above) documents FACT complex membership through automated methods. Both evidence codes are valid. Reason: Duplicate annotations with different evidence codes are acceptable in GO. The IEA source (InterPro) provides orthogonal confirmation of FACT complex membership. Both IBA and IEA annotations should be retained. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | KEEP AS NON CORE | Summary: SPT16 engages in multiple specific protein-protein interactions documented through mass spectrometry and other methods. However, 'protein binding' is a generic term that doesn't specify the functional nature of these interactions. Reason: Per GO curation guidelines, 'protein binding' is discouraged when more specific molecular function terms are available. SPT16's interactions are better characterized through specific terms like 'histone binding' (GO:0042393), 'nucleosome binding' (GO:0031491), and 'identical protein binding' (GO:0042802). These IPI annotations document real interactions but the term lacks specificity. Retain but mark non-core. Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. |
| GO:0005515 protein binding | IPI PMID:11927560 The Paf1 complex physically and functionally associates with... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:11927560 The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. |
| GO:0005515 protein binding | IPI PMID:11927560 The Paf1 complex physically and functionally associates with... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:11927560 The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. |
| GO:0005515 protein binding | IPI PMID:12077334 Yng1p modulates the activity of Sas3p as a component of the ... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:12077334 Yng1p modulates the activity of Sas3p as a component of the yeast NuA3 Hhistone acetyltransferase complex. |
| GO:0005515 protein binding | IPI PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevi... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. |
| GO:0005515 protein binding | IPI PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevi... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. |
| GO:0005515 protein binding | IPI PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevi... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. |
| GO:0005515 protein binding | IPI PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevi... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. |
| GO:0005515 protein binding | IPI PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevi... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. |
| GO:0005515 protein binding | IPI PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevi... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. |
| GO:0005515 protein binding | IPI PMID:14759368 High-definition macromolecular composition of yeast RNA-proc... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:14759368 High-definition macromolecular composition of yeast RNA-processing complexes. |
| GO:0005515 protein binding | IPI PMID:14759368 High-definition macromolecular composition of yeast RNA-proc... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:14759368 High-definition macromolecular composition of yeast RNA-processing complexes. |
| GO:0005515 protein binding | IPI PMID:16299494 A phosphatase complex that dephosphorylates gammaH2AX regula... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:16299494 A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery. |
| GO:0005515 protein binding | IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:20489023 A global protein kinase and phosphatase interaction network in yeast. |
| GO:0005515 protein binding | IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome. | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:21179020 Defining the budding yeast chromatin-associated interactome. |
| GO:0005515 protein binding | IPI PMID:31582854 FACT mediates cohesin function on chromatin. | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:31582854 FACT mediates cohesin function on chromatin. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | KEEP AS NON CORE | Summary: Multiple instances of the same GO:0005515 term with different specific interaction partners from IntAct database. Reason: Each IPI annotation documents real protein-protein interactions with different partners, but the generic 'protein binding' term obscures the specificity of individual interactions. More specific terms would be preferable. Retain these annotations as non-core given availability of more specific binding terms. Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome. |
| GO:0042802 identical protein binding | IPI PMID:14759368 High-definition macromolecular composition of yeast RNA-proc... | KEEP AS NON CORE | Summary: SPT16 forms homodimeric interactions documented through mass spectrometry (PMID:14759368). However, SPT16 primarily functions as a heterodimer with POB3 in the FACT complex. Reason: While the identical protein binding annotation is technically supported by the IPI evidence, SPT16's primary functional form is the heterodimer with POB3. The homodimeric interaction may reflect database artifacts or may occur under specialized conditions. This annotation should be retained but marked non-core as it does not capture the primary functional form. SPT16 forms obligate heterodimer with POB3 according to UniProt and extensive literature, but can interact with itself as documented in IntAct. Supporting Evidence: PMID:14759368 High-definition macromolecular composition of yeast RNA-processing complexes. |
| GO:0042802 identical protein binding | IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome. | KEEP AS NON CORE | Summary: SPT16 forms homodimeric interactions documented through chromatin-associated interactome studies (PMID:21179020). However, SPT16 primarily functions as a heterodimer with POB3. Reason: While the identical protein binding annotation is technically supported by the IPI evidence, SPT16's primary functional form is the heterodimer with POB3. Retain but mark non-core as homodimeric interaction is not the primary functional mode. Supporting Evidence: PMID:21179020 Defining the budding yeast chromatin-associated interactome. |
| GO:0006261 DNA-templated DNA replication | NAS PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 t... | ACCEPT | Summary: DNA-templated DNA replication is directly facilitated by SPT16/FACT. NAS (non-traceable author statement) from ComplexPortal reference is appropriate for this well-characterized function. Reason: SPT16/FACT involvement in DNA replication is extensively documented. The protein associates with replication machinery (MCM2-7, Pol alpha), facilitates fork progression, and mediates parental histone recycling to daughter strands. Multiple studies document this function. Supporting Evidence: PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. |
| GO:0034728 nucleosome organization | NAS PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 t... | ACCEPT | Summary: Nucleosome organization during DNA replication is a key SPT16 function, complementary to its transcriptional roles. Reason: This represents nucleosome management during replication, distinct from (though overlapping with) transcriptional nucleosome organization. Both processes are central to FACT function and well-documented in the literature. Supporting Evidence: PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. |
| GO:1902275 regulation of chromatin organization | NAS PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 t... | ACCEPT | Summary: SPT16/FACT actively regulates chromatin organization by controlling nucleosome structure and positioning throughout the genome. Reason: This term appropriately captures FACT's regulatory role in chromatin dynamics. The protein doesn't merely disassemble and reassemble nucleosomes passively but actively orchestrates their organization in response to biological requirements. This is distinct from and more accurate than the more passive 'nucleosome organization' term. Supporting Evidence: PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. |
| GO:0006325 chromatin organization | IDA PMID:19683499 yFACT induces global accessibility of nucleosomal DNA withou... | ACCEPT | Summary: Chromatin organization is a primary direct activity of SPT16 demonstrated through direct biochemical and cell biological assays. Reason: IDA evidence from direct assays (PMID:19683499) documents SPT16's role in chromatin organization. The protein's ability to facilitate nucleosomal DNA accessibility and reorganize chromatin structure is directly demonstrated. This is core function. Supporting Evidence: PMID:19683499 yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement. |
| GO:0000785 chromatin | IDA PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential... | ACCEPT | Summary: SPT16 localizes to chromatin and is a structural component of chromatin-associated FACT complexes. Reason: Direct evidence from PMID:10413469 documents that SPT16 is chromatin-associated, nuclear, and copurifies with chromatin. This is a valid cellular component annotation with strong experimental support. Supporting Evidence: PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. |
| GO:0007063 regulation of sister chromatid cohesion | IDA PMID:31582854 FACT mediates cohesin function on chromatin. | ACCEPT | Summary: SPT16/FACT regulates sister chromatid cohesion through cooperation with cohesin complex on chromatin. Reason: PMID:31582854 provides direct experimental evidence that FACT mediates cohesin function on chromatin. This annotation represents a documented but more specialized function of SPT16 beyond its primary transcription/replication roles. The annotation is scientifically valid. Supporting Evidence: PMID:31582854 Cohesin is a regulator of genome architecture with roles in sister chromatid cohesion and chromosome compaction. |
| GO:0035101 FACT complex | IGI PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucl... | ACCEPT | Summary: SPT16 is part of the FACT complex, demonstrated through genetic interaction studies where loss of SPT16 affects nucleosome-binding complex assembly. Reason: IGI evidence (genetic interaction with NHP6 - PMID:11432837) documents FACT complex assembly. SPT16 cooperates with NHP6 proteins to form the nucleosome-binding SPN complex. This genetic evidence properly supports the complex assembly annotation. Supporting Evidence: PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. |
| GO:0035101 FACT complex | IPI PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucl... | ACCEPT | Summary: SPT16 physically interacts with POB3 (with column SGD:S000004534) to form the FACT heterodimer, directly demonstrated. Reason: IPI evidence documents the obligate SPT16-POB3 interaction that forms the core of the FACT complex. This is well-established biochemically and is an essential part of SPT16 function. Supporting Evidence: PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. |
| GO:0005515 protein binding | IPI PMID:27226635 The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Hist... | KEEP AS NON CORE | Summary: SPT16 interacts with Mot1 ATPase as documented in the context of transcriptional regulation through preinitiation complex assembly. Reason: While this specific interaction with Mot1 is documented (PMID:27226635), the generic 'protein binding' term obscures the functional significance of this interaction. This annotation should be retained but marked non-core given more specific binding terms are available. Supporting Evidence: PMID:27226635 The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. |
| GO:0003682 chromatin binding | IDA PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential... | ACCEPT | Summary: Chromatin binding is a direct biochemical activity of SPT16, demonstrated through binding assays. Reason: IDA evidence from PMID:10413469 directly shows SPT16 binds to chromatin. This molecular function annotation is supported by direct experimental evidence. The 'contributes_to' relationship indicates this is one of multiple activities rather than the sole function. Supporting Evidence: PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. |
| GO:0006261 DNA-templated DNA replication | IPI PMID:9199353 The Saccharomyces cerevisiae DNA polymerase alpha catalytic ... | ACCEPT | Summary: SPT16 participates in DNA replication through physical interaction with DNA polymerase alpha, directly demonstrated. Reason: IPI evidence from PMID:9199353 documents SPT16's interaction with Pol1 (DNA polymerase alpha) catalytic subunit, establishing a direct physical link to replication machinery. This supports SPT16's functional involvement in replication processes. Supporting Evidence: PMID:9199353 The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein. file:yeast/SPT16/SPT16-deep-research-falcon.md - FACT is reported to physically interact with **DNA polymerase Ξ±** in yeast. |
| GO:0006334 nucleosome assembly | IDA PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 t... | ACCEPT | Summary: Nucleosome assembly is a core molecular function of SPT16/FACT, demonstrated through direct biochemical assays showing nucleosome deposition activity. Reason: IDA evidence from PMID:12952948 documents SPT16's role in nucleosome assembly. The protein actively facilitates reassembly of nucleosomes following polymerase passage and during DNA replication. This is a primary and essential function. Supporting Evidence: PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. |
| GO:0006334 nucleosome assembly | IDA PMID:15082784 Structural features of nucleosomes reorganized by yeast FACT... | ACCEPT | Summary: Nucleosome assembly is a core molecular function of SPT16/FACT, demonstrated through structural studies of FACT-reorganized nucleosomes. Reason: IDA evidence from PMID:15082784 documents structural features of nucleosomes reorganized by FACT, demonstrating SPT16's role in nucleosome assembly. Multiple evidence sources strengthen this annotation. Supporting Evidence: PMID:15082784 Structural features of nucleosomes reorganized by yeast FACT and its HMG box component, Nhp6. |
| GO:0031491 nucleosome binding | IDA PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucl... | ACCEPT | Summary: Nucleosome binding is a core molecular function of SPT16, directly demonstrated through biochemical assays. Reason: IDA evidence from PMID:11432837 directly documents SPT16 nucleosome binding. The protein's multiple histone-binding domains enable this core activity. The 'contributes_to' relationship appropriately reflects that this is part of the multi-domain histone chaperone activity. Supporting Evidence: PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. |
| GO:0042393 histone binding | IDA PMID:18089575 Structural and functional analysis of the Spt16p N-terminal ... | ACCEPT | Summary: Histone binding is a core molecular function of SPT16, with direct biochemical evidence of interactions with histone H3, H4, H2A, and H2B. Reason: IDA evidence from PMID:18089575 directly documents histone binding. The N-terminal domain binds H3-H4, middle domain binds H3-H4 tetramers, and C-terminal domain binds H2A-H2B dimers. These interactions are structural and mechanistically essential for nucleosome chaperone function. Supporting Evidence: PMID:18089575 Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits. file:yeast/SPT16/SPT16-deep-research-falcon.md - a **middle domain** that contacts **(H3βH4)β**, file:yeast/SPT16/SPT16-deep-research-falcon.md FACT/Spt16 is described as atypical because it engages both major histone modules, enabling coordinated nucleosome disassembly/reassembly: |
| GO:0045899 positive regulation of RNA polymerase II transcription preinitiation complex assembly | IDA PMID:15987999 The yeast FACT complex has a role in transcriptional initiat... | ACCEPT | Summary: SPT16/FACT has a direct role in preinitiation complex assembly and transcription initiation through FACT-mediated nucleosome disassembly at promoters. Reason: IDA evidence from PMID:15987999 directly demonstrates FACT's role in transcription initiation. The protein facilitates PIC assembly by clearing nucleosomal barriers at promoters and promoting TBP binding to TATA boxes. This is distinct from and complementary to elongation functions. Supporting Evidence: PMID:15987999 The yeast FACT complex has a role in transcriptional initiation. file:yeast/SPT16/SPT16-deep-research-falcon.md In yeast, Spt16/FACT is a nucleosome-templated transcription factor that promotes productive RNAPII elongation, supports nucleosome disassembly and reassembly during polymerase passage, suppresses cryptic initiation, and contributes to promoter function/PIC formation. |
| GO:0060261 positive regulation of transcription initiation by RNA polymerase II | IGI PMID:15987999 The yeast FACT complex has a role in transcriptional initiat... | ACCEPT | Summary: SPT16 positively regulates transcription initiation by RNA polymerase II through genetic interaction with initiation factors. Reason: IGI evidence from PMID:15987999 documents functional interaction between SPT16 and transcription initiation machinery. The genetic interactions establish SPT16's role in promoting initiation. This complements the direct IDA evidence. Supporting Evidence: PMID:15987999 The yeast FACT complex has a role in transcriptional initiation. |
| GO:0060261 positive regulation of transcription initiation by RNA polymerase II | IMP PMID:19574230 FACT and the proteasome promote promoter chromatin disassemb... | ACCEPT | Summary: SPT16 positively regulates transcription initiation by RNA Pol II, demonstrated through mutation/depletion studies showing defects in initiation when SPT16 is inactivated. Reason: IMP evidence from PMID:19574230 documents that promoter chromatin disassembly and transcriptional initiation require both FACT and proteasome function. Loss of FACT function impairs initiation, supporting this annotation with the strongest type of mechanistic evidence. Supporting Evidence: PMID:19574230 FACT and the proteasome promote promoter chromatin disassembly and transcriptional initiation. |
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