NAP1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000785 chromatin	IBA GO_REF:0000033	ACCEPT	Summary: Manual review: chromatin is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0005634 nucleus	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Nap1 functions in both the cytosol and the nucleus. Falcon deep research notes that Nap1 is mostly cytoplasmic but also functions in the nucleus, where it supports nucleosome assembly and remodeling; nuclear activity is genuine but the protein is predominantly cytosolic, so this localization is retained as non-core. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md but also acts in the nucleus where it supports targeted histone release/import, nucleosome assembly and remodeling during transcription
GO:0006334 nucleosome assembly	IBA GO_REF:0000033	ACCEPT	Summary: Nucleosome assembly is a core biological process for NAP1. Falcon deep research supports that Nap1 is a conserved nucleosome assembly protein that promotes correct nucleosome organization by delivering H2A-H2B dimers into nucleosomes rather than allowing random histone-DNA association. Reason: Retained as supported or plausible for this gene and evidence context. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 is proposed to recruit H2A-H2B to maintain ordered nucleosome arrangement
GO:0042393 histone binding	IBA GO_REF:0000033	ACCEPT	Summary: Histone binding is a core molecular function of NAP1. Falcon deep research confirms the primary substrate is the H2A-H2B dimer, which Nap1 binds with nanomolar affinity as a stable homodimer, shielding the basic DNA-binding surfaces of the histones. Reason: Retained as supported or plausible for this gene and evidence context. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md The primary substrate of Nap1 is the H2A–H2B dimer file:yeast/NAP1/NAP1-deep-research-falcon.md Nagae et al. describe Nap1 as a ~48 kDa monomer that forms a stable homodimer and binds a single H2A–H2B dimer with nanomolar affinity
GO:0003682 chromatin binding	IBA GO_REF:0000033	ACCEPT	Summary: Manual review: chromatin binding is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0003677 DNA binding	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: Manual review: DNA binding may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0005634 nucleus	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: Manual review: nucleus may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Manual review: cytoplasm is the predominant steady-state localization of NAP1 and the principal site of its core H2A-H2B chaperone activity. Reason: Accepted as core, consistent with the IDA cytoplasm annotation (PMID:7622566); the cytoplasm is the predominant steady-state localization where Nap1 carries out its core H2A-H2B chaperone activity.
GO:0005935 cellular bud neck	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Manual review: cellular bud neck may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0005940 septin ring	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: Manual review: septin ring may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0006334 nucleosome assembly	IEA GO_REF:0000002	ACCEPT	Summary: Manual review: nucleosome assembly is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0005515 protein binding	IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:12058072 Cell cycle-dependent assembly of a Gin4-septin complex.	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:14645854 ATP-driven exchange of histone H2AZ variant catalyzed by SWR...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:14759368 High-definition macromolecular composition of yeast RNA-proc...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:15045029 A protein complex containing the conserved Swi2/Snf2-related...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:16299494 A phosphatase complex that dephosphorylates gammaH2AX regula...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:18467557 An in vivo map of the yeast protein interactome.	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:18719252 High-quality binary protein interaction map of the yeast int...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:19172749 Histone chaperone specificity in Rtt109 activation.	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:19536198 An atlas of chaperone-protein interactions in Saccharomyces ...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:20489023 A global protein kinase and phosphatase interaction network ...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome.	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:23468594 A safeguard mechanism regulates Rho GTPases to coordinate cy...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:25416945 A memory system of negative polarity cues prevents replicati...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:37968396 The social and structural architecture of the yeast protein ...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:9214386 Control of mitotic events by Nap1 and the Gin4 kinase.	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding	IPI PMID:9813092 The septins are required for the mitosis-specific activation...	MARK AS OVER ANNOTATED	Summary: Manual review: protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0042802 identical protein binding	IPI PMID:16432217 The structure of nucleosome assembly protein 1.	MARK AS OVER ANNOTATED	Summary: Manual review: identical protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0042802 identical protein binding	IPI PMID:18467557 An in vivo map of the yeast protein interactome.	MARK AS OVER ANNOTATED	Summary: Manual review: identical protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0042802 identical protein binding	IPI PMID:18719252 High-quality binary protein interaction map of the yeast int...	MARK AS OVER ANNOTATED	Summary: Manual review: identical protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0042802 identical protein binding	IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome.	MARK AS OVER ANNOTATED	Summary: Manual review: identical protein binding is too generic or over-extended for NAP1. Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0140597 protein carrier chaperone	IDA PMID:31062022 Tsr4 and Nap1, two novel members of the ribosomal protein ch...	ACCEPT	Summary: Manual review: protein carrier chaperone is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0000511 H2A-H2B histone complex chaperone activity	IDA PMID:39601790 Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted...	ACCEPT	Summary: This is the core molecular function of NAP1. Falcon deep research (anchored on Fung et al. 2024, the source of this PMID) establishes that Nap1 forms a stable homodimer that binds H2A-H2B, shields their DNA-binding surfaces, and cooperates with the importin Kap114 and RanGTP to chaperone H2A-H2B for nucleosome assembly, forming a quaternary Nap1_2-H2A-H2B-Kap114-RanGTP complex. Reason: Retained as supported or plausible for this gene and evidence context. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 forms a stable homodimer file:yeast/NAP1/NAP1-deep-research-falcon.md Kap114, H2A–H2B, and Nap1\_2 form equimolar complexes, including a quaternary Nap1\_2•H2A–H2B•Kap114•RanGTP assembly
GO:0006334 nucleosome assembly	IDA PMID:39601790 Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted...	ACCEPT	Summary: Manual review: nucleosome assembly is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0000511 H2A-H2B histone complex chaperone activity	IDA PMID:27225933 Structural evidence for Nap1-dependent H2A-H2B deposition an...	ACCEPT	Summary: Manual review: H2A-H2B histone complex chaperone activity is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0006334 nucleosome assembly	IDA PMID:27225933 Structural evidence for Nap1-dependent H2A-H2B deposition an...	ACCEPT	Summary: Manual review: nucleosome assembly is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0000920 septum digestion after cytokinesis	NAS PMID:12058072 Cell cycle-dependent assembly of a Gin4-septin complex.	KEEP AS NON CORE	Summary: Manual review: septum digestion after cytokinesis may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0000921 septin ring assembly	NAS PMID:12058072 Cell cycle-dependent assembly of a Gin4-septin complex.	KEEP AS NON CORE	Summary: Manual review: septin ring assembly may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0006607 NLS-bearing protein import into nucleus	IMP PMID:12456659 A role for nucleosome assembly protein 1 in the nuclear tran...	KEEP AS NON CORE	Summary: Nap1 participates in histone H2A-H2B nuclear import in cooperation with the importin Kap114 and the Ran-GTP system. Falcon deep research describes Nap1 escorting H2A-H2B and facilitating targeted release onto assembling nucleosomes in the nucleus. This nuclear-import function is real but is an extension of the core H2A-H2B chaperone activity rather than the gene's primary function. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 interacts with importin Kap114 and Ran-pathway components to escort H2A-H2B and facilitate targeted release onto assembling nucleosomes/tetrasomes in the nucleus
GO:0042274 ribosomal small subunit biogenesis	IGI PMID:31062022 Tsr4 and Nap1, two novel members of the ribosomal protein ch...	KEEP AS NON CORE	Summary: Manual review: ribosomal small subunit biogenesis may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0051082 unfolded protein binding	IDA PMID:31062022 Tsr4 and Nap1, two novel members of the ribosomal protein ch...	KEEP AS NON CORE	Summary: The IDA supporting this term comes from PMID:31062022, which identifies Nap1 as a dedicated chaperone for the ribosomal protein Rps6/eS6, promoting its solubility in vitro - not for H2A-H2B. 'Unfolded protein binding' is a defensible generic description of that r-protein chaperoning activity, so the term is retained, but it is peripheral to Nap1's core H2A-H2B histone chaperone function (GO:0000511, GO:0042393), which is independently supported by PMID:39601790 and PMID:27225933. Re-terming this specific annotation to GO:0000511 would misattribute Rps6-chaperone evidence to the histone chaperone function. Reason: Retained as non-core because it describes Nap1's peripheral ribosomal-protein (Rps6/eS6) chaperone activity, consistent with the KEEP_AS_NON_CORE treatment of the other PMID:31062022-derived annotation (GO:0042274 ribosomal small subunit biogenesis). Supporting Evidence: PMID:31062022 We report the identification of Nap1 and Tsr4 as direct binding partners of Rps6 and Rps2, respectively. Both factors promote the solubility of their r-protein clients in vitro. PMID:31062022 Nap1 interacts with a large, mostly eukaryote-specific binding surface of Rps6
GO:0005737 cytoplasm	IDA PMID:30341817 Septin-associated proteins Aim44 and Nis1 traffic between th...	ACCEPT	Summary: Manual review: cytoplasm is the predominant steady-state localization of NAP1 and the principal site of its core H2A-H2B chaperone activity. Reason: Accepted as core, consistent with the other cytoplasm annotations; the cytoplasm is the predominant steady-state localization where Nap1 carries out its core H2A-H2B chaperone activity. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 is described as the principal cytosolic H2A–H2B chaperone that is mostly cytoplasmic but also functions in the nucleus (implying nucleocytoplasmic shuttling)
GO:0032174 cellular bud neck septin collar	IDA PMID:30341817 Septin-associated proteins Aim44 and Nis1 traffic between th...	KEEP AS NON CORE	Summary: Manual review: cellular bud neck septin collar may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0032153 cell division site	IDA PMID:25416945 A memory system of negative polarity cues prevents replicati...	KEEP AS NON CORE	Summary: Manual review: cell division site may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0098841 protein localization to cell division site after cytokinesis	IMP PMID:25416945 A memory system of negative polarity cues prevents replicati...	KEEP AS NON CORE	Summary: Manual review: protein localization to cell division site after cytokinesis may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0006334 nucleosome assembly	IDA PMID:1400414 Functional analysis of nucleosome assembly protein, NAP-1. T...	ACCEPT	Summary: Manual review: nucleosome assembly is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0008047 enzyme activator activity	IDA PMID:22308335 Histone density is maintained during transcription mediated ...	KEEP AS NON CORE	Summary: Manual review: enzyme activator activity may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0031116 positive regulation of microtubule polymerization	IMP PMID:7622567 NAP1 acts with Clb1 to perform mitotic functions and to supp...	KEEP AS NON CORE	Summary: Manual review: positive regulation of microtubule polymerization may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0005737 cytoplasm	IDA PMID:7622566 Members of the NAP/SET family of proteins interact specifica...	ACCEPT	Summary: Cytoplasm is the predominant localization of Nap1. Falcon deep research describes Nap1 as the principal cytosolic H2A-H2B chaperone that handles newly synthesized H2A-H2B before nuclear import, implying nucleocytoplasmic shuttling. This is the major site of action even though Nap1 also functions in the nucleus. Reason: Accepted as core. The cytoplasm is the predominant steady-state localization of Nap1 and the principal site of its core H2A-H2B histone-chaperone activity, where Nap1 handles newly synthesized H2A-H2B before nuclear import. Falcon deep research (Fung et al. 2024) describes Nap1 as the principal cytosolic H2A-H2B chaperone that is mostly cytoplasmic, so this IDA localization is elevated from non-core to a core location. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 is described as the principal cytosolic H2A–H2B chaperone that is mostly cytoplasmic but also functions in the nucleus (implying nucleocytoplasmic shuttling)
GO:0006334 nucleosome assembly	IDA PMID:2016313 Identification and molecular cloning of yeast homolog of nuc...	ACCEPT	Summary: Manual review: nucleosome assembly is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0006337 nucleosome disassembly	IDA PMID:16492771 Chromatin remodeling by nucleosome disassembly in vitro.	ACCEPT	Summary: Nucleosome disassembly via H2A-H2B eviction is a genuine Nap1 activity. Falcon deep research (anchored on Nagae et al. 2023) shows that Nap1 can dismantle an H2A-H2B dimer from a partially unwrapped nucleosome, with its acidic C-terminal flexible tails engaging an otherwise buried histone interface via a 'penetrating fuzzy binding' mechanism; removal is slow from fully wrapped nucleosomes but greatly accelerated by translocase-induced partial DNA unwrapping. Reason: Retained as supported or plausible for this gene and evidence context. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 can also act in H2A–H2B eviction/dismantling, particularly when nucleosomal DNA is partially unwrapped file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 acidic C-terminal flexible tails can engage an H2A–H2B interface that is normally buried in the nucleosome file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 can remove H2A–H2B from fully wrapped nucleosomes only slowly at low temperature, but removal is accelerated when DNA is partially unwrapped
GO:0007117 budding cell bud growth	IMP PMID:13680156 Saccharomyces cerevisiae Ats1p interacts with Nap1p, a cytop...	KEEP AS NON CORE	Summary: Manual review: budding cell bud growth may be context-dependent or peripheral for NAP1. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0030332 cyclin binding	IPI PMID:7622566 Members of the NAP/SET family of proteins interact specifica...	KEEP AS NON CORE	Summary: Nap1 binds the B-type cyclin Clb2, linking its histone-chaperone activity to mitotic regulation and suppression of polar bud growth. Falcon deep research notes these reported functional interactions with mitotic regulators (Clb2 and Gin4). This is a peripheral, organism-specific function rather than the core chaperone activity, so it is retained as non-core. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md Nap1 physically/functionally interacts with mitotic regulators including Clb2 and Gin4, linking histone-chaperone activity to mitotic functions and suppression of polar bud growth
GO:0032968 positive regulation of transcription elongation by RNA polymerase II	IDA PMID:22308335 Histone density is maintained during transcription mediated ...	KEEP AS NON CORE	Summary: Nap1 supports transcription-coupled chromatin dynamics by managing H2A-H2B during polymerase passage. Falcon deep research shows that partial nucleosome unwrapping by a translocase dramatically facilitates Nap1-mediated H2A-H2B dimer dismantling, consistent with a role in nucleosome disassembly/reassembly cycles linked to transcription. This is a downstream consequence of the core chaperone activity rather than a primary function. Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function. Supporting Evidence: file:yeast/NAP1/NAP1-deep-research-falcon.md partial nucleosome unwrapping by a translocase dramatically facilitates Nap1-mediated H2A–H2B dimer dismantling
GO:0042393 histone binding	IDA PMID:17289584 Chz1, a nuclear chaperone for histone H2AZ.	ACCEPT	Summary: Manual review: histone binding is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.
GO:0042393 histone binding	IDA PMID:21348863 Assembly states of the nucleosome assembly protein 1 (NAP-1)...	ACCEPT	Summary: Manual review: histone binding is consistent with known biology of NAP1. Reason: Retained as supported or plausible for this gene and evidence context.

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

Falcon

📚 Additional Documentation

Notes

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