| Functional role/process | Molecular mechanism (substrate/partner) | Subcellular localization | Key experimental evidence type | Key quantitative/statistical findings (if any) | Key source (first author, year, journal, DOI/URL) |
|---|---|---|---|---|---|
| Canonical nucleosome assembly / histone chaperoning | Nap1 is a conserved nucleosome assembly protein and core histone chaperone that preferentially handles H2A-H2B dimers and supports nucleosome organization during transcription and replication (pqac-00000008, pqac-00000009) | Cytosol and nucleus/chromatin-associated; largely cytoplasmic but functions in nucleus (pqac-00000010) | In vitro nucleosome assembly studies; yeast deletion genetics; genome-wide expression profiling (pqac-00000008, pqac-00000009, pqac-00000020) | In nap1Δ cells, ~8.4-12.0% of ORFs changed by ≥2-fold across three experiments; ~10% in one experiment (pqac-00000020) | Ohkuni, 2003, *Biochemical and Biophysical Research Communications*, https://doi.org/10.1016/S0006-291X(03)00907-0 |
| H2A-H2B chaperone / shielding of basic histones | Nap1 dimer (Nap1₂ / “Nap12”) binds H2A-H2B, shields DNA-binding surfaces, prevents nonspecific histone-DNA aggregation, and promotes specific nucleosome incorporation; cooperates with Kap114 (pqac-00000010, pqac-00000028) | Mainly cytosolic for newly synthesized H2A-H2B, with nuclear transfer/assembly functions (pqac-00000010, pqac-00000028) | Immunoprecipitation from cytosolic and RanGTP-rich nuclear extracts; SEC-MALS; AUC; pull-downs; cryo-EM; DNA competition and nucleosome assembly assays (pqac-00000010, pqac-00000019, pqac-00000028) | 1:1 Kap114:Nap1₂ complex; 1:1:1 Kap114:Nap1₂:H2A-H2B complex; quaternary 1:1:1:1 Kap114:Nap1₂:H2A-H2B:RanGTP complex; cryo-EM at 2.9 Å (local refinement 4.0 Å) (pqac-00000019) | Fung, 2024, *Journal of Cell Biology*, https://doi.org/10.1083/jcb.202408193 |
| Nucleocytoplasmic co-chaperone for histone import and targeted nuclear release | Nap1 interacts with importin Kap114 and Ran-pathway components to escort H2A-H2B and facilitate targeted release onto assembling nucleosomes/tetrasomes in the nucleus (pqac-00000010, pqac-00000028, pqac-00000032) | Nucleocytoplasmic shuttling; cytosol and nucleus (pqac-00000010, pqac-00000028) | Genetics; IP; biochemical reconstitution; cryo-EM; model of histone transfer pathway (pqac-00000010, pqac-00000028, pqac-00000032) | Kap114-H2A-H2B interface ~1,600 Ų; Kap114-Nap1₂ interface ~120 Ų; Nap1 β-hairpin residues E288/R290/Q292 are critical for Kap114 binding and nuclear localization (pqac-00000019) | Fung, 2024, *Journal of Cell Biology*, https://doi.org/10.1083/jcb.202408193 |
| Transcription-coupled nucleosome disassembly / H2A-H2B eviction | Nap1 can dismantle an H2A/H2B dimer from a partially unwrapped nucleosome; acidic flexible C-terminal tails access buried histone interfaces via a “penetrating fuzzy binding” mechanism, especially after translocase-induced DNA unwrapping (pqac-00000012, pqac-00000029) | Likely nuclear/chromatin during transcription-associated collisions (inferred from in vitro nucleosome-translocase assays) (pqac-00000012, pqac-00000029) | In vitro transcription assays with T7 RNAP on nucleosomes; EMSA; MNase assays; Ni-NTA pull-downs; coarse-grained molecular simulations (pqac-00000012, pqac-00000024, pqac-00000029) | Nap1 is a ~48 kDa monomer forming a stable homodimer; full Nap1 model used residues 1-417 with globular core 74-365; slow dismantling from fully wrapped nucleosomes reported on hour timescales at 4°C, but greatly accelerated by partial unwrapping (pqac-00000011, pqac-00000022) | Nagae, 2023, *Nucleic Acids Research*, https://doi.org/10.1093/nar/gkad396 |
| Maintenance of in vivo nucleosome spacing and clustered transcriptional states | Nap1 is proposed to recruit H2A-H2B to maintain ordered nucleosome arrangement, influencing whether adjacent gene regions are relatively “tight” (repressed) or “loose” (expressed) (pqac-00000009) | Nuclear chromatin (functional inference from transcriptional and nucleosome phenotypes) (pqac-00000009, pqac-00000020) | Affymetrix Yeast Genome S98 microarrays; cluster analysis of nap1Δ expression profiles (pqac-00000016, pqac-00000020) | Among genes changing >2-fold in nap1Δ, ~35.4% were in clusters versus 12.7% in nbp2Δ and 12.5% in htr1Δ; genome-wide clustered proportions in two experiments were 28.3-30.7% for nap1Δ vs 14.8-18.1% in comparators (pqac-00000016) | Ohkuni, 2003, *Biochemical and Biophysical Research Communications*, https://doi.org/10.1016/S0006-291X(03)00907-0 |
| Cell-cycle / mitotic regulation linkage | Nap1 physically/functionally interacts with mitotic regulators including Clb2 and Gin4, linking histone-chaperone activity to mitotic functions and suppression of polar bud growth (pqac-00000008, pqac-00000009) | Cytoplasm and nucleus; exact compartment for all interactions not resolved in provided excerpts (pqac-00000008, pqac-00000010) | Prior yeast interaction studies summarized in genome-wide and review-style discussion (pqac-00000008, pqac-00000009) | No direct numeric effect size provided in the extracted passages for this interaction class (pqac-00000008, pqac-00000009) | Ohkuni, 2003, *Biochemical and Biophysical Research Communications*, https://doi.org/10.1016/S0006-291X(03)00907-0 |
| Experimental reagent/platform for chromatin reconstitution and mechanistic studies | Purified yeast Nap1 is used in nucleosome reconstitution, chromatin transcription assays, histone-DNA competition tests, structural biology, and simulation-supported mechanistic studies (pqac-00000024, pqac-00000028, pqac-00000029) | In vitro implementation rather than endogenous cellular localization (pqac-00000024, pqac-00000028) | Reconstituted Widom 601 nucleosomes; T7 RNAP assays; EMSA; MNase; SEC-MALS; cryo-EM; MD simulations (pqac-00000024, pqac-00000028, pqac-00000029) | Example assay conditions: 6 µM Nap1 dimers, 0.2 µM nucleosomes, 0.8 µM T7 RNAP, 200 mM NaCl; simulations placed Nap1 ~80 Å from nucleosome (pqac-00000022, pqac-00000024) | Nagae, 2023, *Nucleic Acids Research*, https://doi.org/10.1093/nar/gkad396; Fung, 2024, *Journal of Cell Biology*, https://doi.org/10.1083/jcb.202408193 |


*Table: This table summarizes experimentally supported functions, mechanisms, localization, and quantitative findings for Saccharomyces cerevisiae NAP1 (UniProt P25293; YKR048C). It is useful as a compact evidence map for functional annotation focused on the yeast protein rather than similarly named proteins in other organisms.*