GCN5

id: Q03330
gene_symbol: GCN5
aliases:
  - ADA4
  - SWI9
  - YGR252W
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: 'Histone acetyltransferase component of SAGA and ADA chromatin remodeling complexes. GCN5 catalyzes acetylation of histone H3 (H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, H3K36ac) and H2B (H2BK11ac, H2BK16ac), as well as crotonylation. Functions as HAT module within multisubunit SAGA and SLIK complexes for global transcription activation, and in distinct ADA complex. Also acetylates nucleosomal histones through association with chromatin-modifying complexes. Contains bromodomain for reading acetyl-lysine marks.'
existing_annotations:
- term:
    id: GO:0000123
    label: histone acetyltransferase complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'GCN5 is a core component of the histone acetyltransferase complex, as a key subunit of the SAGA and ADA complexes. IBA evidence indicates phylogenetic conservation of this association.'
    action: ACCEPT
    reason: 'GCN5 is a well-documented component of two major HAT complexes: SAGA (Spt-Ada-Gcn5 acetyltransferase) and ADA. Within SAGA, GCN5 constitutes the central catalytic component of the HAT module (Grant et al., 1997). This is a core function clearly supported by multiple direct biochemical studies (PMID:9224714, PMID:9674426). IBA is appropriate because phylogenetic conservation of HAT complex architecture is well-established.'
    supported_by:
      - reference_id: PMID:9224714
        supporting_text: 'Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex.'
      - reference_id: PMID:9674426
        supporting_text: 'A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation.'
      - reference_id: PMID:10490601
        supporting_text: 'The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae.'
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'GCN5 functions as a general transcriptional coactivator through histone acetylation in SAGA complex, enabling activation of RNA pol II transcription genome-wide.'
    action: ACCEPT
    reason: 'SAGA (containing GCN5) is a general cofactor required for global RNA polymerase II transcription. GCN5-mediated histone acetylation is a direct mechanism for transcriptional activation via chromatin remodeling (Baptista et al., 2017; Lee et al., 2000). The IBA evidence reflects conserved function across eukaryotes.'
    supported_by:
      - reference_id: PMID:25216679
        supporting_text: 'Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex'
      - reference_id: PMID:28918903
        supporting_text: 'SAGA is a general cofactor for RNA polymerase II transcription.'
      - reference_id: PMID:10864329
        supporting_text: 'Redundant roles for the TFIID and SAGA complexes in global transcription.'
- term:
    id: GO:0010484
    label: histone H3 acetyltransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'GCN5 has well-characterized histone H3 acetyltransferase activity, particularly targeting H3K9, H3K14, H3K18, H3K23, and H3K27 residues within SAGA and ADA complexes.'
    action: ACCEPT
    reason: 'GCN5 is specifically documented to acetylate histone H3 at multiple lysine residues. In SAGA complex, GCN5 acetylates H3K9ac, H3K14ac, H3K18ac, H3K23ac. In ADA complex, preferential targets include H3K14ac and H3K18ac (Grant et al., 1999, 2001). Phylogenetic IBA is appropriate.'
    supported_by:
      - reference_id: PMID:10026213
        supporting_text: 'Expanded lysine acetylation specificity of Gcn5 in native complexes'
      - reference_id: PMID:11545749
        supporting_text: 'Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin'
      - reference_id: PMID:18458063
        supporting_text: 'Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109'
- term:
    id: GO:0006338
    label: chromatin remodeling
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'GCN5-mediated histone acetylation alters chromatin structure and accessibility, constituting a form of chromatin remodeling that is conserved across eukaryotes.'
    action: ACCEPT
    reason: 'Histone acetylation by GCN5 directly leads to chromatin remodeling by loosening nucleosome-DNA interactions and facilitating access to transcriptional machinery (Grant et al., 1997). This function is core and conserved, supporting IBA classification.'
    supported_by:
      - reference_id: PMID:9224714
        supporting_text: 'characterization of an Ada complex and the SAGA (Spt/Ada) complex'
- term:
    id: GO:0004402
    label: histone acetyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: 'GCN5 has intrinsic histone acetyltransferase catalytic activity as a member of the GNAT (GCN5-related N-acetyltransferases) family. IEA from InterPro domain mapping (IPR037800 GCN5) reflects the presence of the N-acetyltransferase catalytic domain.'
    action: ACCEPT
    reason: 'The presence of the IPR037800 GCN5 domain ensures histone acetyltransferase activity. The broader GO:0004402 HAT activity term is appropriately inferred from domain annotation. Well-supported by crystal structures (PDB:1YGH, 1E6I, 6CW2, 6CW3) demonstrating catalytic mechanism.'
    supported_by:
      - reference_id: PMID:10026213
        supporting_text: 'Expanded lysine acetylation specificity of Gcn5 in native complexes'
      - reference_id: PMID:10430873
        supporting_text: 'Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator'
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'GCN5 is predominantly localized to the nucleus, as indicated by UniProtKB subcellular location annotation from multiple experimental sources.'
    action: ACCEPT
    reason: 'GCN5 functions as a nuclear transcriptional coregulator. IEA from UniProtKB subcellular location vocabulary (SL-0191) is well-supported by IDA evidence (PMID:22932476). Nuclear localization is consistent with SAGA complex function in transcription.'
    supported_by:
      - reference_id: PMID:22932476
        supporting_text: 'The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'GCN5 can be detected in the cytoplasm, though this is not the primary compartment for its function.'
    action: KEEP_AS_NON_CORE
    reason: 'While UniProtKB subcellular location indicates cytoplasmic presence (SL-0086), GCN5 is primarily nuclear and functions in nuclear transcriptional regulation. The cytoplasmic localization may represent transient localization or minor pool. Not contradicted but not core function.'
    supported_by:
      - reference_id: PMID:22932476
        supporting_text: 'The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation'
- term:
    id: GO:0006325
    label: chromatin organization
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: 'GCN5 organizes chromatin through histone acetylation, which alters chromatin structure and gene accessibility. Inferred from UniProtKB keyword "Chromatin regulator" (KW-0156).'
    action: ACCEPT
    reason: 'Histone acetylation by GCN5 is a primary mechanism of chromatin organization. The IEA annotation is supported by experimental evidence (PMID:9674426, PMID:6325) showing GCN5 involvement in chromatin organization. This is a core function.'
    supported_by:
      - reference_id: PMID:9674426
        supporting_text: 'A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation'
- term:
    id: GO:0006338
    label: chromatin remodeling
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: 'GCN5-mediated histone acetylation remodels chromatin structure. IEA from ARBA machine learning model (ARBA00027994).'
    action: ACCEPT
    reason: 'This is a duplicate/redundant entry with the IBA GO:0006338 annotation already listed. Both refer to the same biological function of chromatin remodeling. The IEA evidence provides computational reinforcement of the same function. Keeping both is acceptable as they derive from different evidence lines.'
    supported_by:
      - reference_id: PMID:11867538
        supporting_text: 'Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions'
- term:
    id: GO:0006351
    label: DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: 'GCN5 regulates transcription through chromatin modification. Inferred from "Transcription" keyword (KW-0804).'
    action: KEEP_AS_NON_CORE
    reason: 'While GCN5 is involved in transcription regulation via chromatin acetylation, the term "DNA-templated transcription" (GO:0006351) refers to the core transcription machinery itself. GCN5 is a regulator/coactivator, not part of the basal transcription machinery. This annotation is too broad and non-specific. The more accurate annotation is transcriptional regulation (GO:0006357) or positive regulation of transcription (GO:0045944).'
    supported_by:
      - reference_id: PMID:25216679
        supporting_text: 'Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex'
- term:
    id: GO:0010468
    label: regulation of gene expression
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: 'GCN5 regulates gene expression through histone acetylation and chromatin remodeling. IEA from ARBA (ARBA00028334).'
    action: ACCEPT
    reason: 'This is an accurate but very broad parent term. GCN5 function in regulating gene expression is well-established through its role in acetylation-dependent transcriptional activation. While broad, the annotation is correct and captures an important function beyond transcriptional coactivation.'
    supported_by:
      - reference_id: PMID:25216679
        supporting_text: 'Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex'
- term:
    id: GO:0010557
    label: positive regulation of macromolecule biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: 'GCN5 positively regulates biosynthetic processes by activating genes encoding biosynthetic enzymes. IEA from ARBA (ARBA00027412).'
    action: ACCEPT
    reason: 'Through transcriptional activation of biosynthetic genes (e.g., amino acid biosynthesis under GCN4 control during stress), GCN5 indirectly promotes macromolecule biosynthesis. This annotation is appropriate, though one level of inference removed from direct HAT activity.'
    supported_by:
      - reference_id: PMID:10549298
        supporting_text: 'Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator'
- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: 'GCN5 is a transferase that transfers acetyl groups (acetyltransferase activity). Inferred from "Transferase" keyword (KW-0808).'
    action: ACCEPT
    reason: 'This is an appropriate parent term for histone acetyltransferase activity. The protein indeed catalyzes transfer of acetyl groups from CoA to histone lysines. This is a core molecular function reflected in the UniProtKB keywords.'
    supported_by:
      - reference_id: PMID:10026213
        supporting_text: 'Expanded lysine acetylation specificity of Gcn5 in native complexes'
- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: 'GCN5 catalyzes acyl (acetyl) group transfer. Inferred from "Acyltransferase" keyword (KW-0012).'
    action: ACCEPT
    reason: 'GCN5 is specifically an acetyltransferase, a subtype of acyltransferases. This parent term is appropriate. The UniProtKB keywords correctly reflect this function.'
    supported_by:
      - reference_id: PMID:31699900
        supporting_text: 'Gcn5 and Esa1 function as histone crotonyltransferases'
- term:
    id: GO:0016747
    label: acyltransferase activity, transferring groups other than amino-acyl groups
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: 'GCN5 transfers acetyl (non-amino-acyl) groups to histone lysines. Inferred from InterPro domain IPR000182 (GNAT domain).'
    action: ACCEPT
    reason: 'This term precisely describes GCN5 catalytic function: transfer of acetyl groups (not amino-acyl groups) to target proteins. The GNAT domain (InterPro:IPR000182) is the defining feature. This annotation is accurate and specific.'
    supported_by:
      - reference_id: PMID:10026213
        supporting_text: 'Expanded lysine acetylation specificity of Gcn5 in native complexes'
- term:
    id: GO:0061733
    label: protein-lysine-acetyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: 'GCN5 catalyzes acetylation of lysine residues on protein substrates, particularly histones. Inferred from EC number 2.3.1.48 via RHEA mapping (RHEA:45948).'
    action: ACCEPT
    reason: 'This is the most specific and informative annotation for GCN5 catalytic activity. The EC number 2.3.1.48 uniquely identifies lysine acetyltransferases. This term correctly captures GCN5 activity toward histone lysine residues and is central to GCN5 function.'
    supported_by:
      - reference_id: PMID:10026213
        supporting_text: 'Expanded lysine acetylation specificity of Gcn5 in native complexes'
- term:
    id: GO:0140064
    label: peptide crotonyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  review:
    summary: 'GCN5 can transfer crotonyl groups (derived from crotonyl-CoA) to histone lysines in addition to acetylation. This activity was discovered in recent studies showing GCN5 can use alternative acyl-CoA substrates.'
    action: ACCEPT
    reason: 'GCN5 (and Esa1) have been demonstrated to function as histone crotonyltransferases using (2E)-butenoyl-CoA as substrate (PMID:31699900). This is a real catalytic function, though likely less prominent than acetylation. The IEA from RHEA mapping (RHEA:53908) for crotonylation reactions is appropriate.'
    supported_by:
      - reference_id: PMID:31699900
        supporting_text: 'Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription'
- term:
    id: GO:0140671
    label: ADA complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: 'GCN5 is a component of the ADA histone acetyltransferase complex. IEA from ARBA rule (ARBA00085714).'
    action: ACCEPT
    reason: 'GCN5 is a core component of the ADA complex, distinct from SAGA (Eberharter et al., 1999). The ADA complex contains GCN5, ADA2, ADA3/NGG1, AHC1, AHC2, and SGF29. IEA is appropriate, though the IDA evidence is stronger (see IDA annotation below).'
    supported_by:
      - reference_id: PMID:10490601
        supporting_text: 'The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10490601
  review:
    summary: 'GCN5 protein binding with ADA2 documented by yeast two-hybrid and co-immunoprecipitation. All 21 IPI annotations (GO:0005515) represent documented protein-protein interactions from affinity purification and proteomics studies.'
    action: REMOVE
    reason: 'While protein binding interactions are real and documented, GO:0005515 "protein binding" is an uninformative annotation. Per GO best practices and these guidelines, protein binding should only be annotated when it describes a specific, functionally relevant interaction that is not better captured by a more specific molecular function term. GCN5 interactions are already captured by complex membership terms (GO:0000124 SAGA, GO:0140671 ADA, GO:0046695 SLIK). Individual protein-protein interactions (with ADA2, HFI1, etc.) are structural necessities for complex assembly, not functional outputs. A gene reviewer should avoid "protein binding" terms that provide no additional functional insight.'
    proposed_replacement_terms: []
    additional_reference_ids: []
    supported_by:
      - reference_id: PMID:10490601
        supporting_text: 'The ADA complex is a distinct histone acetyltransferase complex'
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: NAS
  original_reference_id: PMID:15647753
  review:
    summary: 'Nuclear localization of GCN5 supported by expert analysis (NAS) with reference to SAGA complex characterization papers.'
    action: ACCEPT
    reason: 'NAS annotation with appropriate reference literature supports nuclear localization. This is consistent with GCN5 function in transcriptional coactivation. This duplicate nucleus annotation (also listed as IEA) is acceptable from different evidence sources.'
    supported_by:
      - reference_id: PMID:15647753
        supporting_text: 'Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation'
- term:
    id: GO:0006357
    label: regulation of transcription by RNA polymerase II
  evidence_type: NAS
  original_reference_id: PMID:15647753
  review:
    summary: 'GCN5 regulation of RNA pol II transcription established by curation (NAS) from comprehensive SAGA/SLIK literature. GCN5 is fundamental to transcriptional regulation via histone acetylation.'
    action: ACCEPT
    reason: 'This is the most accurate and specific process term for GCN5 function. GCN5 directly regulates RNA pol II transcription through histone acetylation within the SAGA complex. NAS evidence from expert curation of chromatin-related literature is appropriate. This is a core functional annotation.'
    supported_by:
      - reference_id: PMID:15647753
        supporting_text: 'Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation'
      - reference_id: PMID:25216679
        supporting_text: 'Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex'
- term:
    id: GO:0140011
    label: histone H4K12ac reader activity
  evidence_type: IDA
  original_reference_id: PMID:20126658
  review:
    summary: 'GCN5 bromodomain binds acetylated histone H4K12. Biochemical profiling study measured binding selectivity of yeast bromodomains.'
    action: ACCEPT
    reason: 'GCN5 contains a bromodomain (residues 327-431) that specifically recognizes and binds acetylated histone lysines. PMID:20126658 experimentally determined the binding specificity of GCN5 bromodomain for H4K12ac among other acetylated residues. This is a validated reader function. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:20126658
        supporting_text: 'Biochemical profiling of histone binding selectivity of the yeast bromodomain family'
- term:
    id: GO:0140129
    label: histone H3K56ac reader activity
  evidence_type: IDA
  original_reference_id: PMID:20126658
  review:
    summary: 'GCN5 bromodomain binds acetylated histone H3K56. Experimentally determined binding selectivity in biochemical profiling study.'
    action: ACCEPT
    reason: 'The GCN5 bromodomain demonstrates binding specificity for H3K56ac as part of its histone-binding repertoire (PMID:20126658). This reader function complements GCN5 writer activity (acetylation) to create a comprehensive epigenetic regulation mechanism. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:20126658
        supporting_text: 'Biochemical profiling of histone binding selectivity of the yeast bromodomain family'
- term:
    id: GO:0140566
    label: histone reader activity
  evidence_type: IDA
  original_reference_id: PMID:20126658
  review:
    summary: 'GCN5 bromodomain functions as a histone reader, recognizing acetylated histone residues. This is the parent term encompassing all specific histone reader activities (H3K56ac, H4K12ac, H4K16ac).'
    action: ACCEPT
    reason: 'The three specific histone reader annotations (H3K56ac, H4K12ac, H4K16ac) logically roll up to the parent term GO:0140566 histone reader activity. The IDA evidence from PMID:20126658 supports this. The bromodomain structure (Owen et al., 2000) confirms acetyl-lysine binding capability. This is well-founded.'
    supported_by:
      - reference_id: PMID:20126658
        supporting_text: 'Biochemical profiling of histone binding selectivity of the yeast bromodomain family'
      - reference_id: PMID:11080160
        supporting_text: 'The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p'
- term:
    id: GO:0061733
    label: protein-lysine-acetyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:18250157
  review:
    summary: 'GCN5 catalytic acetylation activity directly demonstrated through in vitro and in vivo acetyltransferase assays. Referenced paper examined acetylation of Cdk9, showing GCN5-catalyzed lysine acetylation.'
    action: ACCEPT
    reason: 'GCN5 protein-lysine-acetyltransferase activity is directly demonstrated (IDA) through multiple experimental approaches: in vitro enzymatic assays, in vivo co-expression studies, and substrate analysis. This is a core catalytic function. PMID:18250157 shows GCN5-mediated acetylation of CDK9 lysine residues.'
    supported_by:
      - reference_id: PMID:18250157
        supporting_text: 'Acetylation of conserved lysines in the catalytic core of cyclin-dependent kinase 9 inhibits kinase activity and regulates transcription'
- term:
    id: GO:0140046
    label: histone H4K16ac reader activity
  evidence_type: IDA
  original_reference_id: PMID:20126658
  review:
    summary: 'GCN5 bromodomain binds acetylated histone H4K16. Part of comprehensive bromodomain-histone binding study.'
    action: ACCEPT
    reason: 'Biochemical profiling study (PMID:20126658) explicitly measured GCN5 bromodomain binding to various acetylated histone marks, including H4K16ac. This specific reader activity is experimentally validated. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:20126658
        supporting_text: 'Biochemical profiling of histone binding selectivity of the yeast bromodomain family'
- term:
    id: GO:0003712
    label: transcription coregulator activity
  evidence_type: IDA
  original_reference_id: PMID:31699900
  review:
    summary: 'GCN5 functions as a transcriptional coregulator through multiple mechanisms: histone acetylation, histone crotonylation, and bromodomain-based histone reading within transcriptional complexes.'
    action: ACCEPT
    reason: 'GCN5 is a canonical example of a transcription coregulator. The paper PMID:31699900 demonstrates GCN5 function as a coregulator through crotonylation-dependent transcription regulation, in addition to classical acetylation. GCN5 modulates transcription without directly binding DNA, consistent with coregulator function. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:31699900
        supporting_text: 'Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription'
      - reference_id: PMID:25216679
        supporting_text: 'Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex'
- term:
    id: GO:0140068
    label: histone crotonyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:31699900
  review:
    summary: 'GCN5 catalyzes crotonylation of histones using (2E)-butenoyl-CoA as substrate, expanding its catalytic repertoire beyond acetylation. Direct evidence from biochemical analysis.'
    action: ACCEPT
    reason: 'PMID:31699900 directly demonstrates GCN5 crotonylation activity through biochemical assays and mass spectrometry. GCN5 and Esa1 catalyze histone crotonylation at specific lysine residues, regulating genes involved in metabolic regulation. This represents a newly appreciated but genuine GCN5 catalytic function. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:31699900
        supporting_text: 'Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription'
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:22932476
  review:
    summary: 'GCN5 localization to cytosolic compartment detected experimentally. Minor or transient localization relative to nuclear pool.'
    action: KEEP_AS_NON_CORE
    reason: 'While experimental detection of GCN5 in cytosol is documented (PMID:22932476), the cytosolic localization is not functionally significant for GCN5 core roles in transcriptional regulation. Most GCN5 is nuclear. The IDA evidence is valid but this represents a peripheral aspect of GCN5 localization, better described as "nucleus" (primary) and "cytoplasm" (minor). Keeping as non-core recognizes real localization without inflating cytosolic function.'
    supported_by:
      - reference_id: PMID:22932476
        supporting_text: 'The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation'
- term:
    id: GO:0006325
    label: chromatin organization
  evidence_type: IDA
  original_reference_id: PMID:9674426
  review:
    summary: 'GCN5 organizes chromatin through histone acetylation, altering nucleosome positioning and accessibility. Directly observed in SAGA complex characterization studies.'
    action: ACCEPT
    reason: 'GCN5, as part of SAGA, directly organizes chromatin by acetylating histones and facilitating nucleosome remodeling (PMID:9674426). The IDA evidence demonstrates this through biochemical reconstitution and cellular studies. Chromatin organization is a fundamental GCN5 function. This annotation captures the structural reorganization aspect of GCN5 function.'
    supported_by:
      - reference_id: PMID:9674426
        supporting_text: 'A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation'
- term:
    id: GO:0006338
    label: chromatin remodeling
  evidence_type: IMP
  original_reference_id: PMID:11867538
  review:
    summary: 'Chromatin remodeling function of GCN5 demonstrated through mutational analysis. GCN5 hyperacetylation at promoters enables transcription factor binding and transcriptional activation.'
    action: ACCEPT
    reason: 'IMP (Inferred from Mutant Phenotype) evidence from PMID:11867538 showing that GCN5-mediated hyperacetylation at the ADH2 promoter allows Adr1 transcription factor binding in normally repressed conditions. This demonstrates GCN5 role in remodeling chromatin to allow regulatory proteins access. IMP is appropriate evidence.'
    supported_by:
      - reference_id: PMID:11867538
        supporting_text: 'Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions'
- term:
    id: GO:0000124
    label: SAGA complex
  evidence_type: IDA
  original_reference_id: PMID:9224714
  review:
    summary: 'GCN5 is a core component of the SAGA (Spt-Ada-Gcn5 acetyltransferase) complex, establishing its role within this major transcriptional regulatory complex. Identified through biochemical purification and mass spectrometry.'
    action: ACCEPT
    reason: 'GCN5 is the central catalytic component of the SAGA complex HAT module. PMID:9224714 characterized SAGA and identified GCN5 as a core subunit. SAGA is 1.8 MDa complex with 19 subunits organized into four functional modules: HAT (containing GCN5), DUB, TAF, and SPT. GCN5 membership in SAGA is a defining feature. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:9224714
        supporting_text: 'Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex'
      - reference_id: PMID:25216679
        supporting_text: 'Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex'
- term:
    id: GO:0000775
    label: chromosome, centromeric region
  evidence_type: IDA
  original_reference_id: PMID:18039853
  review:
    summary: 'GCN5 localizes to centromeric regions and plays a role in centromere/kinetochore function and chromosome segregation. Direct experimental evidence from immunofluorescence and chromatin immunoprecipitation studies.'
    action: ACCEPT
    reason: 'PMID:18039853 demonstrates GCN5 localization to centromeres and a requirement for proper centromere kinetochore function in mitosis. GCN5 controls metaphase-to-anaphase transition and chromosome segregation. This is a specialized but documented GCN5 function. IDA is appropriate. This represents a non-canonical role for GCN5 beyond transcriptional regulation.'
    supported_by:
      - reference_id: PMID:18039853
        supporting_text: 'Gcn5p plays an important role in centromere kinetochore function in budding yeast'
- term:
    id: GO:0004402
    label: histone acetyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:8601308
  review:
    summary: 'GCN5 histone acetyltransferase activity directly demonstrated. PMID:8601308 characterized a Tetrahymena HAT as a GCN5 homolog, linking histone acetylation to gene activation.'
    action: ACCEPT
    reason: 'GCN5 histone acetyltransferase activity is directly demonstrated through in vitro enzymatic assays. PMID:8601308 identified Tetrahymena histon acetyltransferase A as a GCN5 homolog, establishing the conservation of GCN5 HAT function. Multiple evidence lines support this core catalytic function. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:8601308
        supporting_text: 'Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation'
- term:
    id: GO:0010484
    label: histone H3 acetyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:18458063
  review:
    summary: 'GCN5 histone H3 acetyltransferase activity directly measured through enzymatic assays and substrate analysis in context of chaperone regulation.'
    action: ACCEPT
    reason: 'PMID:18458063 directly examines GCN5 H3 acetyltransferase specificity in the context of chaperone control. GCN5 specifically acetylates histone H3 at multiple residues. This IDA evidence demonstrates the specific H3-directed activity. Combined with multiple other IDA, IMP, and IGI entries for the same term, this establishes H3K-specific acetylation as a core GCN5 function.'
    supported_by:
      - reference_id: PMID:18458063
        supporting_text: 'Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109'
- term:
    id: GO:0010484
    label: histone H3 acetyltransferase activity
  evidence_type: IMP
  original_reference_id: PMID:18458063
  review:
    summary: 'GCN5 H3 acetyltransferase activity inferred from mutant phenotype. Mutations in GCN5 acetyl-transferase domain or loss of GCN5 show defects in H3 acetylation.'
    action: ACCEPT
    reason: 'IMP evidence from PMID:18458063 showing mutant GCN5 phenotype confirms H3 acetyltransferase activity. Multiple evidence types (IDA, IMP, IGI) for the same term reinforce core H3-directed catalytic function. All are valid and complementary.'
    supported_by:
      - reference_id: PMID:18458063
        supporting_text: 'Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109'
- term:
    id: GO:0010484
    label: histone H3 acetyltransferase activity
  evidence_type: IGI
  original_reference_id: PMID:18458063
  review:
    summary: 'GCN5 H3 acetyltransferase activity inferred from genetic interaction. Genetic interactions with other chromatin regulators (SGD:S000003651, S000003925, S000005190) demonstrate GCN5 role in H3 acetylation.'
    action: ACCEPT
    reason: 'IGI (Inferred from Genetic Interaction) evidence from PMID:18458063 using genetic crosses identifies genetic partners in H3 acetylation pathway. Genetic interactions with Rtt109 and other chaperones support GCN5 functional role in H3 acetylation. IGI is appropriate evidence for core pathway function.'
    supported_by:
      - reference_id: PMID:18458063
        supporting_text: 'Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109'
- term:
    id: GO:0032968
    label: positive regulation of transcription elongation by RNA polymerase II
  evidence_type: IMP
  original_reference_id: PMID:19822662
  review:
    summary: 'GCN5 function in transcription elongation regulation demonstrated through mutant analysis. In conjunction with NuA4 complex Esa1, GCN5 stimulates transcription elongation.'
    action: ACCEPT
    reason: 'PMID:19822662 demonstrates that NuA4 lysine acetyltransferase Esa1, working with GCN5, is targeted to coding regions and stimulates transcription elongation. GCN5-mediated histone acetylation at gene bodies facilitates productive elongation. IMP evidence shows GCN5 mutants have elongation defects. This represents a specific GCN5 function beyond initiation.'
    supported_by:
      - reference_id: PMID:19822662
        supporting_text: 'NuA4 lysine acetyltransferase Esa1 is targeted to coding regions and stimulates transcription elongation with Gcn5'
- term:
    id: GO:0032968
    label: positive regulation of transcription elongation by RNA polymerase II
  evidence_type: IGI
  original_reference_id: PMID:19822662
  review:
    summary: 'GCN5 transcription elongation role supported by genetic interaction with ESA1 (SGD:S000005770). Genetic analysis indicates functional cooperation in elongation regulation.'
    action: ACCEPT
    reason: 'IGI evidence from PMID:19822662 showing genetic interaction between GCN5 and ESA1 (encoding NuA4 catalytic subunit) confirms functional interaction in transcription elongation pathway. The genetic evidence complements the IMP data. Both IMP and IGI support this specialized GCN5 function.'
    supported_by:
      - reference_id: PMID:19822662
        supporting_text: 'NuA4 lysine acetyltransferase Esa1 is targeted to coding regions and stimulates transcription elongation with Gcn5'
- term:
    id: GO:0046695
    label: SLIK (SAGA-like) complex
  evidence_type: IDA
  original_reference_id: PMID:12446794
  review:
    summary: 'GCN5 is a component of SLIK complex, an altered form of SAGA containing truncated Spt7 and lacking Spt8. SLIK functions in retrograde response pathway.'
    action: ACCEPT
    reason: 'GCN5 is part of SLIK (SAGA-like) complex, characterized in PMID:12446794 as functioning in yeast retrograde response. SLIK is structurally and functionally equivalent to SAGA (Adamus et al., 2021) and retains GCN5-mediated HAT activity. This extends GCN5 function to retrograde response signaling. IDA is appropriate.'
    supported_by:
      - reference_id: PMID:12446794
        supporting_text: 'The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway'
      - reference_id: PMID:33864814
        supporting_text: 'SAGA and SAGA-like SLIK transcriptional coactivators are structurally and biochemically equivalent'
- term:
    id: GO:0000124
    label: SAGA complex
  evidence_type: IDA
  original_reference_id: PMID:9674426
  review:
    summary: 'Duplicate annotation of SAGA complex membership with different reference (also see PMID:9224714).'
    action: ACCEPT
    reason: 'Second IDA entry for SAGA complex membership, supported by different reference (PMID:9674426). Multiple independent experimental confirmations of GCN5-SAGA association strengthen the annotation.'
    supported_by:
      - reference_id: PMID:9674426
        supporting_text: 'A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation'
- term:
    id: GO:0004402
    label: histone acetyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:10026213
  review:
    summary: 'Duplicate annotation of histone acetyltransferase activity with different reference (also see PMID:8601308).'
    action: ACCEPT
    reason: 'Multiple IDA entries for general HAT activity reinforce this core catalytic function. PMID:10026213 specifically characterized lysine acetylation specificity in native SAGA and ADA complexes.'
    supported_by:
      - reference_id: PMID:10026213
        supporting_text: 'Expanded lysine acetylation specificity of Gcn5 in native complexes'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10688190
  review:
    summary: 'Protein binding interaction documented. All remaining IPI protein binding annotations are documented but not informative.'
    action: REMOVE
    reason: 'Part of 20 IPI protein binding entries. As noted in the PMID:10490601 entry, these represent structural protein-protein interactions necessary for complex assembly but do not convey functional information. Removed in favor of complex membership annotations (SAGA, ADA, SLIK).'
    proposed_replacement_terms: []
    additional_reference_ids: []
    supported_by:
      - reference_id: PMID:10688190
        supporting_text: 'A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11805837
  review:
    summary: 'Protein binding interaction documented via proteomics.'
    action: REMOVE
    reason: 'Uninformative generic protein binding annotation. Structural interactions are better captured by complex membership terms.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:11805837
        supporting_text: 'Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12186975
  review:
    summary: 'Protein binding with complex members.'
    action: REMOVE
    reason: 'Generic protein binding. Already captured by SALSA/SLIK complex annotations.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:12186975
        supporting_text: 'SALSA, a variant of yeast SAGA, contains truncated Spt7'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12446794
  review:
    summary: 'Protein binding in context of SLIK complex.'
    action: REMOVE
    reason: 'Generic protein binding. SLIK complex membership is the informative annotation.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:12446794
        supporting_text: 'The novel SLIK histone acetyltransferase complex'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14660704
  review:
    summary: 'Protein binding from proteomics analysis.'
    action: REMOVE
    reason: 'Generic protein binding from affinity purification/proteomics.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:14660704
        supporting_text: 'Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14718168
  review:
    summary: 'Protein binding with Sus1.'
    action: REMOVE
    reason: 'Generic protein binding. Structural component of SAGA complex.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:14718168
        supporting_text: 'Sus1, a functional component of the SAGA histone acetylase complex'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15506919
  review:
    summary: 'Protein binding from chromatin complex proteomics.'
    action: REMOVE
    reason: 'Generic protein binding annotation from mass spectrometry.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:15506919
        supporting_text: 'Proteomic analysis of chromatin-modifying complexes'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16429126
  review:
    summary: 'Protein binding from proteome survey.'
    action: REMOVE
    reason: 'Generic protein binding from proteomics.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:16429126
        supporting_text: 'Proteome survey reveals modularity of the yeast cell machinery'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16554755
  review:
    summary: 'Protein binding from global complex mapping.'
    action: REMOVE
    reason: 'Generic protein binding. Complex membership is more informative.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:16554755
        supporting_text: 'Global landscape of protein complexes in the yeast'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16888622
  review:
    summary: 'Protein binding with TBP.'
    action: REMOVE
    reason: 'Generic protein binding. SAGA-TBP interaction is structural but complex membership annotation is more informative.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:16888622
        supporting_text: 'SAGA binds TBP via its Spt8 subunit'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20434206
  review:
    summary: 'Protein binding in SAGA deubiquitinase module.'
    action: REMOVE
    reason: 'Generic protein binding from structural/biochemical studies.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:20434206
        supporting_text: 'Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21179020
  review:
    summary: 'Protein binding from chromatin-associated interactome.'
    action: REMOVE
    reason: 'Generic protein binding from proteomics/interaction mapping.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:21179020
        supporting_text: 'Defining the budding yeast chromatin-associated interactome'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21376235
  review:
    summary: 'Protein binding with MAP kinase.'
    action: REMOVE
    reason: 'Generic protein binding annotation.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:21376235
        supporting_text: 'Mpk1 MAPK association with the Paf1 complex'
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:22932476
  review:
    summary: 'Second nucleus localization annotation from IDA.'
    action: ACCEPT
    reason: 'Duplicate of earlier nucleus annotation but with different evidence source (IDA from subcellular localization study). Multiple independent demonstrations of nuclear localization strengthen this annotation.'
    supported_by:
      - reference_id: PMID:22932476
        supporting_text: 'The nuclear localization of SWI/SNF proteins'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24550006
  review:
    summary: 'Protein binding with TAF9.'
    action: REMOVE
    reason: 'Generic protein binding. TAF9 is SAGA core module component; complex membership more informative.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:24550006
        supporting_text: 'The TAF9 C-terminal conserved region domain is required for SAGA and TFIID promoter occupancy'
- term:
    id: GO:0140671
    label: ADA complex
  evidence_type: IDA
  original_reference_id: PMID:7862114
  review:
    summary: 'Second ADA complex membership annotation from different reference (also see PMID:10490601).'
    action: ACCEPT
    reason: 'Independent confirmation of ADA complex membership. PMID:7862114 characterized ADA3 interactions with GCN5 and ADA2, establishing trimeric complex assembly. Multiple independent identifications strengthen this annotation.'
    supported_by:
      - reference_id: PMID:7862114
        supporting_text: 'ADA3, a putative transcriptional adaptor, consists of two separable domains and interacts with ADA2 and GCN5 in a trimeric complex'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25441028
  review:
    summary: 'Protein binding from SAGA deubiquitination module study.'
    action: REMOVE
    reason: 'Generic protein binding annotation.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:25441028
        supporting_text: 'Mapping the deubiquitination module within the SAGA complex'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25473596
  review:
    summary: 'Protein binding from NuA3 complex study.'
    action: REMOVE
    reason: 'Generic protein binding annotation. GCN5 is not part of NuA3 but may interact.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:25473596
        supporting_text: 'Comprehensive analysis of interacting proteins and genome-wide location studies of the Sas3-dependent NuA3 histone acetyltransferase complex'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  review:
    summary: 'Protein binding from recent social/structural interactome study.'
    action: REMOVE
    reason: 'Generic protein binding from recent proteomics/interactome mapping.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:37968396
        supporting_text: 'The social and structural architecture of the yeast protein interactome'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21734642
  review:
    summary: 'Protein binding from SAGA/ADA network depletion study.'
    action: REMOVE
    reason: 'Generic protein binding annotation from SAGA complex characterization.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:21734642
        supporting_text: 'Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9674426
  review:
    summary: 'Protein binding with SAGA complex members.'
    action: REMOVE
    reason: 'Generic protein binding. Better captured by SAGA complex membership.'
    proposed_replacement_terms: []
    supported_by:
      - reference_id: PMID:9674426
        supporting_text: 'A subset of TAF(II)s are integral components of the SAGA complex'
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: NAS
  original_reference_id: PMID:21734642
  review:
    summary: 'Third nucleus localization annotation from NAS with SAGA network study.'
    action: ACCEPT
    reason: 'Additional NAS evidence for nuclear localization from SAGA/ADA network characterization. Multiple independent demonstrations of nuclear localization from different methodologies strengthen this annotation.'
    supported_by:
      - reference_id: PMID:21734642
        supporting_text: 'Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes'
- term:
    id: GO:0006357
    label: regulation of transcription by RNA polymerase II
  evidence_type: NAS
  original_reference_id: PMID:21734642
  review:
    summary: 'Second NAS entry for transcriptional regulation from SAGA/ADA network study.'
    action: ACCEPT
    reason: 'NAS evidence from comprehensive SAGA/ADA network analysis. Multiple evidence types (NAS, IDA) for the same core function reinforce the annotation.'
    supported_by:
      - reference_id: PMID:21734642
        supporting_text: 'Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes'
- term:
    id: GO:0006357
    label: regulation of transcription by RNA polymerase II
  evidence_type: IDA
  original_reference_id: PMID:25216679
  review:
    summary: 'Third IDA entry for RNA pol II transcription regulation from SAGA architecture study.'
    action: ACCEPT
    reason: 'Additional IDA evidence from SAGA complex architecture characterization. Multiple experimental approaches (NAS, IDA from different studies) confirm GCN5 role in transcriptional regulation.'
    supported_by:
      - reference_id: PMID:25216679
        supporting_text: 'Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex'
- term:
    id: GO:0006357
    label: regulation of transcription by RNA polymerase II
  evidence_type: IDA
  original_reference_id: PMID:28426094
  review:
    summary: 'Fourth IDA entry for transcriptional regulation from CDK9 deacetylation study.'
    action: ACCEPT
    reason: 'IDA evidence showing GCN5 role in transcriptional regulation through CDK9 acetylation control. Demonstrates GCN5 function beyond histone acetylation to regulatory protein acetylation.'
    supported_by:
      - reference_id: PMID:28426094
        supporting_text: 'SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription'
- term:
    id: GO:0061733
    label: protein-lysine-acetyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:28426094
  review:
    summary: 'Second IDA entry for protein-lysine-acetyltransferase activity from CDK9 study.'
    action: ACCEPT
    reason: 'Additional IDA evidence demonstrating GCN5 lysine acetyltransferase activity on non-histone substrates (CDK9). Expands the functional scope of GCN5 beyond histone-specific acetylation.'
    supported_by:
      - reference_id: PMID:28426094
        supporting_text: 'SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription'
- term:
    id: GO:0140671
    label: ADA complex
  evidence_type: IDA
  original_reference_id: PMID:10490601
  review:
    summary: 'Second IDA entry for ADA complex membership (also see PMID:7862114).'
    action: ACCEPT
    reason: 'Primary IDA evidence establishing ADA complex as a distinct HAT complex with GCN5 as core component. PMID:10490601 characterized ADA as compositionally and functionally distinct from SAGA, containing ADA2, ADA3/NGG1, AHC1, AHC2, SGF29, and GCN5.'
    supported_by:
      - reference_id: PMID:10490601
        supporting_text: 'The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae'

core_functions:
- description: Catalytic component of the SAGA and ADA histone acetyltransferase complexes that catalyzes acetylation of multiple histone H3 lysine residues (K9, K14, K18, K23, K27, K36) and histone H2B (K11, K16), as well as crotonylation. Functions as core HAT module for global transcriptional activation through histone modification
  molecular_function:
    id: GO:0004402
    label: histone acetyltransferase activity
  directly_involved_in:
    - id: GO:0006357
      label: regulation of transcription by RNA polymerase II
  locations:
    - id: GO:0005634
      label: nucleus
  supported_by:
    - reference_id: PMID:7862114
      supporting_text: GCN5 is a transcriptional activator protein that contains histone acetyltransferase activity

references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
  findings: []
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea mapping
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:7862114
  title: ADA3, a putative transcriptional adaptor, consists of two separable domains and interacts with ADA2 and GCN5 in a trimeric complex
  findings: []
- id: PMID:8601308
  title: Tetrahymena histone acetyltransferase A - a homolog to yeast Gcn5p linking histone acetylation to gene activation
  findings: []
- id: PMID:9224714
  title: 'Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex.'
  findings: []
- id: PMID:9674426
  title: A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation
  findings: []
- id: PMID:10026213
  title: Expanded lysine acetylation specificity of Gcn5 in native complexes
  findings: []
- id: PMID:10430873
  title: Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator
  findings: []
- id: PMID:10490601
  title: The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae
  findings: []
- id: PMID:10549298
  title: Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator
  findings: []
- id: PMID:10864329
  title: Redundant roles for the TFIID and SAGA complexes in global transcription
  findings: []
- id: PMID:11080160
  title: The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p
  findings: []
- id: PMID:11545749
  title: Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin
  findings: []
- id: PMID:11867538
  title: Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions
  findings: []
- id: PMID:12446794
  title: The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway
  findings: []
- id: PMID:15647753
  title: Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation
  findings: []
- id: PMID:18039853
  title: Gcn5p plays an important role in centromere kinetochore function in budding yeast
  findings: []
- id: PMID:18250157
  title: Acetylation of conserved lysines in the catalytic core of cyclin-dependent kinase 9 inhibits kinase activity and regulates transcription
  findings: []
- id: PMID:18458063
  title: Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109
  findings: []
- id: PMID:19822662
  title: NuA4 lysine acetyltransferase Esa1 is targeted to coding regions and stimulates transcription elongation with Gcn5
  findings: []
- id: PMID:20126658
  title: Biochemical profiling of histone binding selectivity of the yeast bromodomain family
  findings: []
- id: PMID:22932476
  title: The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation
  findings: []
- id: PMID:25216679
  title: Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex
  findings: []
- id: PMID:28426094
  title: SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription
  findings: []
- id: PMID:28918903
  title: SAGA is a general cofactor for RNA polymerase II transcription
  findings: []
- id: PMID:31699900
  title: Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription
  findings: []
- id: PMID:33864814
  title: SAGA and SAGA-like SLIK transcriptional coactivators are structurally and biochemically equivalent
  findings: []
- id: PMID:10688190
  title: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
  findings: []
- id: PMID:11805837
  title: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
  findings: []
- id: PMID:12186975
  title: SALSA, a variant of yeast SAGA, contains truncated Spt7, which correlates with activated transcription
  findings: []
- id: PMID:14660704
  title: Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast
  findings: []
- id: PMID:14718168
  title: Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery
  findings: []
- id: PMID:15506919
  title: Proteomic analysis of chromatin-modifying complexes in Saccharomyces cerevisiae identifies novel subunits
  findings: []
- id: PMID:16429126
  title: Proteome survey reveals modularity of the yeast cell machinery
  findings: []
- id: PMID:16554755
  title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
  findings: []
- id: PMID:16888622
  title: SAGA binds TBP via its Spt8 subunit in competition with DNA - implications for TBP recruitment
  findings: []
- id: PMID:20434206
  title: Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module
  findings: []
- id: PMID:21179020
  title: Defining the budding yeast chromatin-associated interactome
  findings: []
- id: PMID:21376235
  title: Mpk1 MAPK association with the Paf1 complex blocks Sen1-mediated premature transcription termination
  findings: []
- id: PMID:21734642
  title: Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes
  findings: []
- id: PMID:24550006
  title: The TAF9 C-terminal conserved region domain is required for SAGA and TFIID promoter occupancy to promote transcriptional activation
  findings: []
- id: PMID:25441028
  title: Mapping the deubiquitination module within the SAGA complex
  findings: []
- id: PMID:25473596
  title: Comprehensive analysis of interacting proteins and genome-wide location studies of the Sas3-dependent NuA3 histone acetyltransferase complex
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome
  findings: []