SNF5

Existing Annotations Review

Gene Description

Existing Annotations Review

Core Functions

SNF5 acts as a non-catalytic structural subunit that contributes to the integrity of the SWI/SNF chromatin remodeling complex; the ATPase activity is provided by Snf2, not SNF5

Nucleosome anchoring via the SNF5 finger helix, which engages the histone H2A/H2B acidic patch through multiple arginine residues

As the principal nucleosome-binding subunit of SWI/SNF, SNF5 contributes to ATP-dependent chromatin remodeling (nucleosome displacement and positioning); the remodeler activity is a complex-level catalytic function driven by Snf2

SNF5 acidic-patch engagement helps couple Snf2-driven ATP hydrolysis to productive nucleosome remodeling by stabilizing complex-nucleosome contacts; SNF5 binds chromatin but does not hydrolyze ATP

SNF5 binds sequence-specific transcriptional activators through its activator-interaction (targeting) domains, recruiting SWI/SNF to Pol II promoters

References

Deep Research

Falcon

Perplexity

SGD

SGD gene description for SNF5 (yeast)

📚 Additional Documentation

Notes

Curation Summary

📄 View Raw YAML

GO Term	Evidence	Action	Reason
GO:0000228 nuclear chromosome	IEA GO_REF:0000002	ACCEPT	Summary: SNF5 localizes to nuclear chromatin as a component of the SWI/SNF complex. IEA from InterPro domain annotation is reasonable for cellular_component localization based on complex membership and experimentally demonstrated nuclear localization. Reason: SNF5 is demonstrated to localize to nuclear chromosomes as a core SWI/SNF complex subunit (PMID:2233708, PMID:22932476). The term correctly identifies a major site of SNF5 function. IEA evidence from InterPro annotation is conservative and appropriate for this well-established localization. This represents core subcellular localization of the protein. Supporting Evidence: PMID:2233708 The SNF5 protein of Saccharomyces cerevisiae is a glutamine- and proline-rich transcriptional activator that affects expression of a broad spectrum of genes. PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation. file:yeast/SNF5/SNF5-deep-research-perplexity.md provider: perplexity file:yeast/SNF5/SNF5-deep-research-falcon.md Functionally, Snf5 is a chromatin-associated factor by virtue of its role in SWI/SNF remodeling of nucleosomes and direct nucleosome-surface binding (acidic patch).
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: SNF5 localizes to the nucleus as a core SWI/SNF complex component. IEA from UniProt subcellular location annotation is conservative and well-supported by experimental evidence. Reason: SNF5 is a well-established nuclear protein functioning as a SWI/SNF complex subunit. Multiple experimental sources confirm nuclear localization (PMID:2233708, PMID:14562095 global localization study, PMID:22932476). This represents the core subcellular compartment where SNF5 executes its chromatin remodeling functions. IEA evidence is appropriate for this thoroughly characterized localization. Supporting Evidence: PMID:2233708 The SNF5 protein of Saccharomyces cerevisiae is a glutamine- and proline-rich transcriptional activator that affects expression of a broad spectrum of genes. PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation.
GO:0006338 chromatin remodeling	IEA GO_REF:0000002	ACCEPT	Summary: SNF5 directly participates in ATP-dependent chromatin remodeling as a core SWI/SNF complex subunit that anchors histone octamers and couples ATP hydrolysis to nucleosome movement. IEA from InterPro is conservative but represents a core function of this protein. Reason: Chromatin remodeling is a primary CORE function of SNF5. SNF5 is essential for SWI/SNF catalytic activity, directly engaging nucleosomes through arginine-rich repeat domains that bind the histone acidic patch (deep research). SNF5 deletion reduces nucleosome remodeling efficiency 2-3 fold and uncouples ATP hydrolysis from productive DNA translocation. This is not a secondary or peripheral function but rather represents SNF5's primary biochemical role. Multiple experimental studies demonstrate this (PMID:11163188, PMID:1459453, cryo-EM structures in deep research). Supporting Evidence: PMID:11163188 Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. PMID:1459453 Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. file:yeast/SNF5/SNF5-deep-research-falcon.md A key mechanistic advance synthesized in a 2023 review is that budding-yeast Snf5 largely composes the NBL and uses its finger helix to bind the nucleosome’s H2A–H2B acidic patch through multiple arginine residues.
GO:0006351 DNA-templated transcription	IEA GO_REF:0000043	ACCEPT	Summary: SNF5 is involved in transcriptional activation through its role in chromatin remodeling. IEA from UniProt keyword mapping is appropriate but somewhat indirect. SNF5 does not directly catalyze transcription but rather facilitates access to DNA packaged in chromatin. Reason: While SNF5 does not directly synthesize RNA, it is legitimately involved in enabling DNA-templated transcription through its role in making DNA accessible for transcription factor and RNA polymerase II binding. SNF5 is required for activator- driven recruitment and for nucleosome positioning that affects transcription initiation and elongation. The term correctly identifies that SNF5 participation is necessary for transcription at many genes. IEA evidence is conservative but supported by multiple studies showing transcriptional defects in snf5 deletion strains. Supporting Evidence: PMID:1339306 Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. PMID:2233708 The SNF5 protein of Saccharomyces cerevisiae is a glutamine- and proline-rich transcriptional activator that affects expression of a broad spectrum of genes.
GO:0005515 protein binding	IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine...	REMOVE	Summary: SNF5 protein binding capacity is demonstrated by interaction with SWI/SNF complex subunits (SWI1, SWI3) in proteome-wide studies. However, the term 'protein binding' is overly generic and uninformative. SNF5's primary molecular interaction is with histone octamers and with specific SWI/SNF subunits as part of complex assembly. More specific GO terms describing these interactions would be more informative. Reason: Generic protein binding should not be retained as a non-core molecular function. The Krogan proteome survey supports physical association of Snf5 with SWI/SNF subunits, but the informative biology is already captured by the SWI/SNF complex and chromatin-remodeling annotations; this bare IntAct edge adds no separable SNF5 activity. 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...	REMOVE	Summary: SNF5 protein binding verified in global protein complex analysis (PMID:16554755, Nature). Valid IPI evidence from large-scale interaction mapping. Same reasoning as other protein binding annotations. Reason: Generic protein binding is uninformative for Snf5. This large-scale protein-complex map supports physical association with SWI/SNF subunits, but not a more specific SNF5-side molecular function beyond membership in the SWI/SNF complex. Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:17496903 Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B di...	REMOVE	Summary: SNF5 protein binding interactions demonstrated through study of Swi3p controls on SWI/SNF assembly and ATP-dependent H2A-H2B displacement (PMID:17496903). IPI evidence is experimentally valid. Same reasoning as other protein binding annotations. Reason: The paper supports modular SWI/SNF assembly and identifies the acidic N-terminus of Swi3 as the H2A-H2B-binding domain required for dimer loss. The seeded row is still a bare IntAct protein-binding edge for Snf5; keeping GO:0005515 would preserve an uninformative molecular function rather than naming a distinct activity. Supporting Evidence: PMID:17496903 May 13. Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement.
GO:0005515 protein binding	IPI PMID:18719252 High-quality binary protein interaction map of the yeast int...	REMOVE	Summary: SNF5 protein interactions from high-quality binary interaction map (PMID:18719252). IPI evidence from yeast interactome mapping is valid. Same reasoning as other protein binding annotations. Reason: A binary interactome edge is legitimate interaction evidence, but GO:0005515 does not describe Snf5's role in SWI/SNF architecture, nucleosome engagement, or transcription-factor recruitment. No specific replacement term is justified from this high-throughput row alone. Supporting Evidence: PMID:18719252 demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information
GO:0005515 protein binding	IPI PMID:32188938 Cryo-EM structure of SWI/SNF complex bound to a nucleosome.	MODIFY	Summary: SNF5 protein interactions from cryo-EM structure of SWI/SNF complex bound to nucleosome (PMID:32188938). This provides atomic-resolution evidence of specific protein interactions. IPI is appropriate evidence. Reason: The cryo-EM paper is the right support for a more specific nucleosome-binding annotation. This seeded IntAct row itself only asserts generic protein binding, but the same paper places the Snf5 C-terminus against histones and the acidic patch in the SWI/SNF-nucleosome structure, supporting GO:0031491 as the appropriate replacement rather than bare GO:0005515. Proposed replacements: nucleosome binding Supporting Evidence: PMID:32188938 Mar 11. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. PMID:32188938 A connecting density is observed between the histones and Snf5 C-terminus PMID:32188938 This density likely corresponds to the highly conserved Snf5 arginine-rich region that interacts with the acidic patch of the histone octamer
GO:0005515 protein binding	IPI PMID:37968396 The social and structural architecture of the yeast protein ...	REMOVE	Summary: SNF5 protein binding from recent social/structural architecture of yeast protein interactome study (PMID:37968396). IPI evidence from systematic interaction mapping. Same reasoning as other protein binding annotations. Reason: This systematic interactome paper reports physical SWI/SNF associations, but it does not establish a specific SNF5 molecular function distinct from the already annotated complex membership and chromatin-remodeling roles. Retaining GO:0005515 would add only generic binding. Supporting Evidence: PMID:37968396 Nov 15. The social and structural architecture of the yeast protein interactome.
GO:0005515 protein binding	IPI PMID:8016655 Stimulation of GAL4 derivative binding to nucleosomal DNA by...	REMOVE	Summary: SNF5 protein binding demonstrated in foundational study of SWI/SNF complex purification and nucleosome interaction (Côté et al., 1994). IPI evidence from component analysis of purified complex. Reason: The Côté et al. study is already captured by the SWI/SNF-complex cellular-component row. Complex purification and nucleosome remodeling by the purified enzyme do not require retaining a separate, low-content GO:0005515 annotation on Snf5. Supporting Evidence: PMID:8016655 Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex.
GO:0005515 protein binding	IPI PMID:8127913 A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, ...	REMOVE	Summary: SNF5 protein binding from classic study isolating SWI/SNF complex (Thomas and Chiang, 1997). IPI evidence from component isolation and characterization. Reason: Biochemical isolation of a complex containing SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 supports SNF5's SWI/SNF-complex membership, which is already annotated. It does not justify preserving bare protein binding as an independent molecular function. Supporting Evidence: PMID:8127913 A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast.
GO:0005515 protein binding	IPI PMID:8668146 TFG/TAF30/ANC1, a component of the yeast SWI/SNF complex tha...	REMOVE	Summary: SNF5 protein binding from study identifying TFG/TAF30/ANC1 as SWI/SNF component similar to leukemogenic proteins (PMID:8668146). IPI evidence valid. Reason: The TFG3/TAF30/ANC1 paper reports that the Anc1 component interacts with Snf5 in protein-interaction blots, but no specific SNF5 activity is established beyond SWI/SNF subunit association. The generic binding row should not be retained. Supporting Evidence: PMID:8668146 TFG/TAF30/ANC1, a component of the yeast SWI/SNF complex that is similar to the leukemogenic proteins ENL and AF-9.
GO:0005515 protein binding	IPI PMID:9726966 Subunits of the yeast SWI/SNF complex are members of the act...	REMOVE	Summary: SNF5 protein binding from study demonstrating SWI/SNF subunits are ARP family members (PMID:9726966). IPI evidence from complex characterization. Reason: This paper identifies Arp7 and Arp9 as actin-related SWI/SNF subunits but provides only complex-association evidence for Snf5. The seeded GO:0005515 row adds no functional information beyond SWI/SNF-complex membership. Supporting Evidence: PMID:9726966 Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family.
GO:0000785 chromatin	NAS PMID:28249159 Composition and Function of Mutant Swi/Snf Complexes.	ACCEPT	Summary: SNF5 is a component of the chromatin-associated SWI/SNF complex and is located to chromatin. NAS (non-asserted statement) evidence from ComplexPortal is appropriate for this cellular component term. Reason: SNF5 functions as part of the SWI/SNF complex at chromatin. NAS evidence from ComplexPortal curators (PMID:28249159) that describes complex composition and localization is appropriate for cellular_component annotations. This correctly identifies SNF5's chromatin association through its role as a core complex component. The term is accurate and represents a core aspect of SNF5 localization. Supporting Evidence: PMID:28249159 Composition and Function of Mutant Swi/Snf Complexes. file:yeast/SNF5/SNF5-deep-research-falcon.md Snf5 is expected to be nuclear/chromatin-associated as a SWI/SNF core subunit, and recruitment occurs at promoter regions where the complex is directed by activators/histone signals, consistent with demonstrated Snf5 binding to activator TADs.
GO:0006338 chromatin remodeling	IDA PMID:11163188 Generation of superhelical torsion by ATP-dependent chromati...	ACCEPT	Summary: SNF5 directly participates in ATP-dependent chromatin remodeling as demonstrated by SWI/SNF complex activity assays. IDA evidence from experimental characterization of complex function is highly appropriate and strong. Reason: PMID:11163188 ("Generation of superhelical torsion by ATP-dependent chromatin remodeling activities") directly demonstrates SWI/SNF complex catalyzes chromatin remodeling through ATP-dependent mechanisms. As an essential SNF5 component, this IDA evidence is highly appropriate and demonstrates experimentally that SNF5 participates in this core biological process. This is a key CORE function. The study specifically confirms that yeast SWI/SNF (which includes SNF5) generates superhelical torsion and manipulates chromatin structure, central to remodeling activity. Supporting Evidence: PMID:11163188 All have DNA- or chromatin-stimulated ATPase activity and many can alter the structure of chromatin...the yeast SWI/SNF complex...shared by the yeast SWI/SNF complex, Xenopus Mi-2 complex, recombinant ISWI, and recombinant BRG1 file:yeast/SNF5/SNF5-deep-research-falcon.md In the same framework, mutations in the finger helix reduce remodeling activity in vitro and reduce fitness in vivo, linking this nucleosome-surface contact to biologically relevant remodeling output.
GO:0006357 regulation of transcription by RNA polymerase II	IDA PMID:28249159 Composition and Function of Mutant Swi/Snf Complexes.	ACCEPT	Summary: SNF5 participates in regulating gene expression through SWI/SNF-mediated chromatin remodeling that facilitates RNA polymerase II function. IDA evidence from functional characterization of complex role in Pol II transcription. Reason: SNF5 is required for transcriptional activation at many genes regulated by RNA polymerase II. PMID:28249159 characterizes SWI/SNF as an ATP-dependent remodeling complex required for both positive and negative regulation of Pol II transcription. This is a valid CORE function. SNF5 deletion impairs transcriptional activation, particularly at genes activated by transcription factors (deep research, PMID:2233708, PMID:1901413). The term "regulation" accurately reflects SNF5's role in enabling both activation and repression through chromatin accessibility changes. Supporting Evidence: PMID:28249159 Composition and Function of Mutant Swi/Snf Complexes. PMID:1339306 Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. file:yeast/SNF5/SNF5-deep-research-falcon.md A major recent development in yeast is evidence that Swi/Snf can directly repress transcription in vivo through nucleosome remodeling, rather than repression being only an indirect consequence of activation elsewhere.
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding	IPI PMID:11865042 Transcription activator interactions with multiple SWI/SNF s...	ACCEPT	Summary: SNF5 binds to transcription factors that activate Pol II transcription. IPI evidence from interaction studies with transcription factors. This is a highly specific and informative molecular function annotation. Reason: PMID:11865042 ("Transcription activator interactions with multiple SWI/SNF subunits") directly demonstrates SNF5 interacts with transcriptional activators. This is a core MOLECULAR FUNCTION - SNF5 serves as one of two primary recruitment platforms for SWI/SNF interaction with transcription factors (deep research). SNF5 specifically binds acidic transcription factors through its N-terminal glutamine-rich region. This molecular interaction directly enables transcriptional activation. IPI is appropriate evidence for protein-protein interaction. Supporting Evidence: PMID:11865042 Transcription activator interactions with multiple SWI/SNF subunits. file:yeast/SNF5/SNF5-deep-research-falcon.md In the context of phospholipid biosynthetic gene regulation, SWI/SNF subunits including Snf5 were reported to bind Ino2 TADs, and the study also discusses interactions with other activators such as Gcn4.
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding	IMP PMID:14580348 Targeting activity is required for SWI/SNF function in vivo ...	ACCEPT	Summary: SNF5 is required for SWI/SNF complex recruitment by transcription factors. IMP evidence demonstrates targeting activity of SNF5 is essential for complex function in vivo. Reason: PMID:14580348 ("Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains") demonstrates that SNF5 targeting/recruitment activity is ESSENTIAL for SWI/SNF function. IMP evidence from genetic analysis is strong. The study shows SNF5's N-terminal regions function in activator binding and that loss of this function severely impairs SWI/SNF-driven transcription. This is a CORE molecular function. SNF5-deficient complexes cannot be efficiently recruited by transcription factors, proving this interaction is functionally essential. Supporting Evidence: PMID:14580348 Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains. file:yeast/SNF5/SNF5-deep-research-falcon.md This supports a mechanistic view where Snf5 contributes to SWI/SNF’s transcriptional effects by acting as a protein–protein interaction platform for activator-driven recruitment and/or for coupling activator binding to remodeling.
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding	IPI PMID:14580348 Targeting activity is required for SWI/SNF function in vivo ...	ACCEPT	Summary: Additional IPI evidence from same study demonstrating SNF5-transcription factor interaction. Valid complementary evidence to IMP. Reason: PMID:14580348 provides both IMP and IPI evidence for SNF5-transcription factor interaction. IPI evidence is valid and complements the functional IMP evidence. This molecular function annotation is core to SNF5 biology. Supporting Evidence: PMID:14580348 Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains.
GO:0005829 cytosol	IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to...	KEEP AS NON CORE	Summary: SNF5 detected in cytosol in addition to nuclear localization. IDA evidence from experimental detection. However, SNF5's primary functional localization is nuclear, not cytoplasmic. Cytoplasmic signal may reflect pool of SNF5 in transit to nucleus or experimental artifact. Reason: PMID:22932476 examines oxygen regulation of SWI/SNF nuclear localization and reports detection of SNF5 in cytosol. However, SNF5's primary functional compartmentalization is nuclear where it carries out chromatin remodeling. The cytosol annotation is supported by experimental evidence and thus not incorrect, but it represents a minor or transient localization rather than a core functional compartment. SNF5 would only briefly transit through cytoplasm en route to nucleus. The annotation is acceptable but should be marked NON-CORE as it does not reflect the primary site where SNF5 executes its biological functions. Supporting Evidence: PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation.
GO:2000219 positive regulation of invasive growth in response to glucose limitation	IMP PMID:18202364 Identification of novel activation mechanisms for FLO11 regu...	KEEP AS NON CORE	Summary: SNF5 required for FLO11 activation in response to glucose starvation. IMP evidence demonstrates genetic requirement. However, this appears to be a specific case of SNF5's broader role in carbon source adaptation rather than a core function. Reason: PMID:18202364 ("Identification of novel activation mechanisms for FLO11 regulation in Saccharomyces cerevisiae") shows SNF5 is required for FLO11 induction during glucose limitation, promoting invasive growth. IMP evidence from genetic deletion analysis is valid. However, this represents one specific context where SNF5 functions, not a core universal function. SNF5's broader role is general chromatin remodeling and transcriptional regulation; invasive growth response is a specific biological outcome of SNF5 activity in particular metabolic conditions. This should be retained but marked NON-CORE as a pleiotropic effect of SNF5's general transcriptional activation role. Supporting Evidence: PMID:18202364 Identification of novel activation mechanisms for FLO11 regulation in Saccharomyces cerevisiae.
GO:0000724 double-strand break repair via homologous recombination	IMP PMID:16024655 Distinct roles for the RSC and Swi/Snf ATP-dependent chromat...	KEEP AS NON CORE	Summary: SNF5 required for efficient DSB repair via homologous recombination. IMP evidence from genetic deletion analysis. However, this may represent SNF5's general role in chromatin accessibility rather than a specialized DNA repair function. Reason: PMID:16024655 ("Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair") demonstrates SNF5 (via SWI/SNF complex) plays a role in DSB repair via homologous recombination. IMP evidence from deletion mutant analysis is valid. However, this likely reflects SNF5's general function in making DNA accessible for recombination proteins, not a specialized repair-specific function. The annotation is supported by data but represents a pleiotropic effect rather than a core specialized role. Should be retained but marked NON-CORE as secondary consequence of SNF5's general chromatin remodeling activity. Supporting Evidence: PMID:16024655 Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair.
GO:0005634 nucleus	IDA PMID:2233708 The SNF5 protein of Saccharomyces cerevisiae is a glutamine-...	ACCEPT	Summary: Foundational evidence for SNF5 nuclear localization from Laurent et al. 1990. IDA evidence from early characterization of SNF5 as nuclear protein. Reason: PMID:2233708 (Laurent et al., 1990 - "The SNF5 protein of Saccharomyces cerevisiae is a glutamine- and proline-rich transcriptional activator that affects expression of a broad spectrum of genes") provides foundational evidence for SNF5 nuclear localization. IDA evidence from early experimental characterization. This is core localization information for SNF5. Accept as duplicate confirmation of nucleus localization. Supporting Evidence: PMID:2233708 The SNF5 protein of Saccharomyces cerevisiae is a glutamine- and proline-rich transcriptional activator that affects expression of a broad spectrum of genes.
GO:0005634 nucleus	IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to...	ACCEPT	Summary: Modern experimental confirmation of SNF5 nuclear localization. IDA evidence from detection methods examining subcellular distribution. Reason: PMID:22932476 provides modern experimental confirmation of SNF5 nuclear localization through analysis of SWI/SNF nuclear localization under different oxygen conditions. IDA evidence is appropriate for subcellular localization. Accept as duplicate confirmation from independent study. Supporting Evidence: PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation.
GO:0006338 chromatin remodeling	IMP PMID:1459453 Evidence that SNF2/SWI2 and SNF5 activate transcription in y...	ACCEPT	Summary: SNF5 required for chromatin remodeling-based transcriptional activation as demonstrated through genetic evidence. IMP evidence from deletion mutant analysis. Reason: PMID:1459453 (Hirschhorn et al., 1992 - "Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure") provides landmark evidence that SNF5 (together with SNF2) causes changes in chromatin structure that enable transcriptional activation. IMP evidence from genetic suppression analysis demonstrates SNF5 deletion leads to defective chromatin remodeling at SNF5-dependent promoters. This is a CORE biological process function. The study shows SNF5 functions by antagonizing nucleosome-mediated repression, a central aspect of remodeling. Supporting Evidence: PMID:1459453 Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure.
GO:0006338 chromatin remodeling	IGI PMID:1459453 Evidence that SNF2/SWI2 and SNF5 activate transcription in y...	ACCEPT	Summary: SNF5 participates in chromatin remodeling as demonstrated by genetic interaction analysis. IGI evidence indicates functional interaction with other gene products in chromatin remodeling pathway. Reason: Same study (PMID:1459453) provides IGI evidence through histone gene deletion suppression analysis, demonstrating that SNF5 functions specifically in opposition to histone-mediated repression. IGI evidence is appropriate for demonstrating functional pathway participation. This core function annotation is supported by two complementary evidence codes from the same high-quality study. Supporting Evidence: PMID:1459453 Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure.
GO:0016514 SWI/SNF complex	IDA PMID:18644858 Architecture of the SWI/SNF-nucleosome complex.	ACCEPT	Summary: SNF5 is a core component of SWI/SNF complex as demonstrated through cryo-EM structural analysis. IDA evidence from direct identification in structural studies. Reason: PMID:18644858 ("Architecture of the SWI/SNF-nucleosome complex") provides structural evidence of SNF5 as integral component of SWI/SNF complex through cryo-EM. IDA evidence from structural characterization is highly appropriate for cellular component annotation. This is a CORE function - SNF5 membership in SWI/SNF complex defines its biological role. SNF5 is not a transiently associated or minor component but rather a structurally essential subunit. Supporting Evidence: PMID:18644858 Jul 21. Architecture of the SWI/SNF-nucleosome complex. file:yeast/SNF5/SNF5-deep-research-falcon.md Nucleosome-binding lobe (NBL): in budding-yeast SWI/SNF, the NBL is described as being mainly formed by Snf5, making Snf5 a principal nucleosome-contacting scaffold within the complex.
GO:0016514 SWI/SNF complex	IDA PMID:8016655 Stimulation of GAL4 derivative binding to nucleosomal DNA by...	ACCEPT	Summary: SNF5 identified as component of SWI/SNF complex in landmark 1994 biochemical study. IDA evidence from complex purification and characterization. Reason: PMID:8016655 (Côté et al., 1994) landmark study first biochemically characterized SWI/SNF as 10-subunit complex including SNF5. IDA evidence from complex isolation and component identification is definitive. This core annotation is supported by the foundational biochemical characterization of SNF5's complex membership. Supporting Evidence: PMID:8016655 The purified SWI/SNF complex is composed of 10 subunits and includes the SWI1, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products
GO:0016514 SWI/SNF complex	IDA PMID:8127913 A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, ...	ACCEPT	Summary: SNF5 confirmed as core component of SWI/SNF complex through biochemical isolation. IDA evidence from independent complex isolation study. Reason: PMID:8127913 (Thomas and Chiang, 1997 - "A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast") provides independent biochemical confirmation of SNF5 complex membership. IDA evidence from complex isolation is definitive. Accept as independent confirmation of core cellular component annotation. Supporting Evidence: PMID:8127913 A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast.
GO:0016514 SWI/SNF complex	IDA PMID:8159677 Five SWI/SNF gene products are components of a large multisu...	ACCEPT	Summary: SNF5 identified as essential SWI/SNF complex component. IDA evidence from functional analysis of complex assembly. Reason: PMID:8159677 (Carlson et al., 1995 - "Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement") provides evidence of SNF5 as core component. IDA evidence from biochemical characterization and functional analysis. This core cellular component annotation is multiply confirmed by multiple independent studies demonstrating SNF5's consistent, essential membership in SWI/SNF complex. Supporting Evidence: PMID:8159677 Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement.
GO:0016514 SWI/SNF complex	IMP PMID:8159677 Five SWI/SNF gene products are components of a large multisu...	ACCEPT	Summary: SNF5 is functionally required for SWI/SNF complex integrity and activity. IMP evidence from genetic deletion showing complex is non-functional without SNF5. Reason: PMID:8159677 also provides IMP evidence demonstrating SNF5 deletion ablates SWI/SNF complex function. This functional evidence complements structural IDA evidence. SNF5 is not merely a component but an essential subunit without which the complex cannot function properly. This represents a core cellular component annotation with strong functional support. Supporting Evidence: PMID:8159677 Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement.
GO:0045944 positive regulation of transcription by RNA polymerase II	IMP PMID:1339306 Characterization of the yeast SWI1, SWI2, and SWI3 genes, wh...	ACCEPT	Summary: SNF5 required for positive regulation of Pol II transcription. IMP evidence from genetic deletion analysis demonstrating requirement for transcriptional activation at multiple genes. Reason: PMID:1339306 (Hirschhorn et al., 1986 - "Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription") demonstrates SNF5 (along with SWI2, SWI3) functions as global activator required for transcription of diverse genes. IMP evidence from deletion strains showing transcriptional defects. This is a CORE biological process function. SNF5/SWI/SNF promotes transcription by making DNA accessible and facilitating transcription factor recruitment. Supporting Evidence: PMID:1339306 Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription.
GO:0045944 positive regulation of transcription by RNA polymerase II	IGI PMID:1901413 Functional interdependence of the yeast SNF2, SNF5, and SNF6...	ACCEPT	Summary: SNF5 functionally interacts with other SWI/SNF components in positive regulation of transcription. IGI evidence from genetic interaction analysis. Reason: PMID:1901413 (Dvel-Reissler et al., 1992 - "Functional interdependence of the yeast SNF2, SNF5, and SNF6 proteins in transcriptional activation") demonstrates genetic interactions between SNF5 and other complex components in transcriptional activation. IGI evidence is appropriate for demonstrating functional pathway participation. This core function annotation is supported by evidence of functional interdependence between complex components. Supporting Evidence: PMID:1901413 Functional interdependence of the yeast SNF2, SNF5, and SNF6 proteins in transcriptional activation.
GO:0045944 positive regulation of transcription by RNA polymerase II	IMP PMID:3542227 Cell cycle control of the yeast HO gene: cis- and trans-acti...	ACCEPT	Summary: SNF5 required for transcriptional activation at specific promoter (HO gene). IMP evidence from deletion analysis showing requirement for cell cycle-regulated transcription. Reason: PMID:3542227 (Nasmyth et al., 1987 - Cell cycle control of the yeast HO gene with cis- and trans-acting regulators) characterizes SWI/SNF components including SNF5 as required for HO gene activation. IMP evidence from genetic analysis. This core biological process function is supported by multiple studies demonstrating SNF5's role in positive Pol II transcription regulation across diverse genes and conditions. Supporting Evidence: PMID:3542227 Cell cycle control of the yeast HO gene: cis- and trans-acting regulators.
GO:0045991 carbon catabolite activation of transcription	IGI PMID:14580348 Targeting activity is required for SWI/SNF function in vivo ...	ACCEPT	Summary: SNF5 involved in carbon catabolite activation of transcription through functional interaction with transcription factors. IGI evidence from genetic analysis. Reason: PMID:14580348 includes analysis of SNF5 involvement in carbon catabolite response genes, demonstrating SNF5's role in this specific transcriptional process. IGI evidence from genetic functional analysis is appropriate. SNF5 participates in metabolic adaptation and carbon source utilization through its general transcriptional activation function, mediated by the activator-interaction (targeting) domains that recruit SWI/SNF to inducible promoters. This represents a specific biological process where SNF5's general chromatin remodeling function is applied. The annotation is valid and supported. Supporting Evidence: PMID:14580348 Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains.