{"gene":"NAP1L1","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2017,"finding":"NAP1L1 enhances CSB-mediated nucleosome remodeling by accelerating the activation and translocation phases, and by decreasing pausing probability during translocation, thereby increasing CSB processivity. NAP1L1 also suppresses CSB's non-productive DNA-binding interactions (including gross DNA distortion).","method":"Single-molecule real-time imaging of nucleosome remodeling; DNA-binding assays with CSB and NAP1L1","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — single-molecule reconstitution with functional validation, multiple orthogonal assays (DNA binding + remodeling kinetics) in one rigorous study","pmids":["28369616"],"is_preprint":false},{"year":2018,"finding":"Nap1l1 knockdown in mouse embryos decreases neural progenitor cell (NPC) proliferation and induces premature neuronal differentiation during cortical development. Nap1l1 promotes SETD1A-mediated H3K4 trimethylation at the RassF10 promoter to upregulate RassF10 expression, and RassF10 overexpression rescues the Nap1l1 KO differentiation defect.","method":"In utero electroporation knockdown; CRISPR-Cas9 knockout mice; RNA-seq; ChIP for H3K4me3 at RassF10 promoter; rescue by RassF10 overexpression","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO mice + knockdown + ChIP + genetic rescue, multiple orthogonal methods in one study","pmids":["29490266"],"is_preprint":false},{"year":2017,"finding":"HCV NS5A interacts with NAP1L1, sequesters it in the cytoplasm blocking its nuclear translocation, and NS5A from genotype 2 (but not genotype 1) additionally targets NAP1L1 for proteasome-mediated degradation. NAP1L1 depletion reduces RELA protein levels and strongly impairs IRF3 TBK1/IKKε-mediated phosphorylation, leading to defective RIG-I and TLR3 antiviral responses.","method":"Co-IP mapping NS5A–NAP1L1 interaction; immunofluorescence for subcellular localization; proteasome inhibitor rescue; siRNA knockdown of NAP1L1 followed by IRF3 phosphorylation and RELA level assays","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, localization imaging, loss-of-function with defined signaling readouts, multiple orthogonal methods","pmids":["28659470"],"is_preprint":false},{"year":2014,"finding":"NAP1L1 binds directly to the p57(Kip2) promoter region (-164 to +21) and promotes its methylation; NAP1L1 silencing decreases p57(Kip2) promoter methylation, upregulates p57(Kip2) transcript and protein, inhibits mTOR pathway phosphorylation, reduces pancreatic NEN cell proliferation in vitro, and decreases tumor size in an orthotopic mouse model.","method":"siRNA/shRNA knockdown; chromatin immunoprecipitation (ChIP) at p57(Kip2) promoter; promoter methylation assay; Western blot for mTOR pathway; orthotopic xenograft model","journal":"Epigenetics & chromatin","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP demonstrating direct promoter binding, methylation assay, in vitro + in vivo KD with defined molecular readouts, multiple orthogonal methods","pmids":["25071868"],"is_preprint":false},{"year":2019,"finding":"NAP1L1 knockdown decreases p53 Lys320 acetylation under normal conditions (attenuating p21 expression and facilitating cell growth), while under genotoxic stress NAP1L1 knockdown increases p53 Lys382 acetylation (enhancing proapoptotic Bax levels and facilitating cell death). Thus NAP1L1 selectively modulates site-specific p53 acetylation to determine cell fate.","method":"siRNA knockdown of NAP1L1 and NAP1L4; Western blot for acetylated p53 at Lys320 and Lys382; p21 and Bax expression assays; cell growth and apoptosis assays under normal and genotoxic stress conditions","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean siRNA KD with site-specific acetylation readouts, two conditions tested, single lab","pmids":["31634504"],"is_preprint":false},{"year":2016,"finding":"KSHV LANA associates with NAP1L1 via its amino-terminal domain in KSHV-infected cells, recruits NAP1L1 to the terminal repeat (TR) region of the viral genome, and this interaction stimulates LANA-mediated DNA replication and TR plasmid persistence. NAP1L1 depletion reduces nucleosome positioning on the viral genome and increases transcription of viral lytic genes.","method":"Co-IP; ChIP from NAP1L1-depleted cells; TR-containing plasmid replication assay; nucleosome positioning assay; reporter assay for LANA-regulated promoters","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, ChIP, functional replication assay, single lab with multiple orthogonal methods","pmids":["27599637"],"is_preprint":false},{"year":2021,"finding":"NAP1L1 interacts with HDGF at the protein level and they co-localize in the cytoplasm; HDGF in turn interacts with the transcription factor c-Jun, which induces expression of cell cycle promoters CCND1/CDK4/CDK6, promoting glioma cell proliferation and cisplatin chemoresistance. HDGF knockdown in NAP1L1-overexpressing cells inhibits proliferation.","method":"Co-IP; immunofluorescence co-localization; siRNA/shRNA knockdown; Western blot for CCND1/CDK4/CDK6; in vitro and in vivo proliferation assays; cisplatin sensitivity assay","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP confirming protein interaction, co-localization, functional rescue experiments, single lab","pmids":["34959221"],"is_preprint":false},{"year":2021,"finding":"NAP1L1 recruits HDGF; HDGF interacts with c-Jun transcription factor to induce CCND1 expression and stimulate HCC cell proliferation. Transfecting HDGF or c-Jun reverses the growth-suppressive effects of NAP1L1 knockdown in HCC cells.","method":"Co-IP; siRNA/shRNA knockdown; Western blot; in vitro and in vivo proliferation assays; rescue transfection of HDGF/c-Jun","journal":"Frontiers in cell and developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, functional rescue, in vivo xenograft, single lab; corroborates findings from other labs on same axis","pmids":["34368121"],"is_preprint":false},{"year":2021,"finding":"NAP1L1 interacts with HDGF (Co-IP and co-localization in cytoplasm), and HDGF recruits c-Jun to induce CCND1 expression and drive proliferation in nasopharyngeal carcinoma. HDGF or c-Jun overexpression rescues growth suppression caused by NAP1L1 knockdown.","method":"Co-IP; immunofluorescence; siRNA/shRNA knockdown; RNA-seq; GSEA; Western blot; in vitro/in vivo proliferation assays; rescue experiments","journal":"Biomedicine & pharmacotherapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, RNA-seq pathway analysis, functional rescue, single lab; replicates NAP1L1–HDGF–c-Jun axis","pmids":["34563951"],"is_preprint":false},{"year":2021,"finding":"NAP1L1 interacts with HDGF (Co-IP, confocal co-localization in cytoplasm); HDGF recruits c-Jun which induces CCND1 expression to drive breast cancer cell proliferation. HDGF overexpression rescues growth suppression from NAP1L1 knockdown.","method":"Co-IP; confocal immunofluorescence; siRNA/shRNA knockdown; MTT/Edu/colony assays; in vivo xenograft; rescue transfection","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and co-localization, functional rescue, in vivo model, single lab; independently replicates NAP1L1–HDGF–c-Jun axis","pmids":["34774047"],"is_preprint":false},{"year":2022,"finding":"NAP1L1 binds to HDGF, recruits DDX5, and induces β-catenin/CCND1 signaling to promote colon cancer cell proliferation. HDGF or DDX5 overexpression restores cell growth in NAP1L1-knockdown colon cancer cells.","method":"Co-IP; siRNA knockdown; MTT/EdU/colony assays; in vivo xenograft; rescue transfection; Western blot for β-catenin/CCND1","journal":"Acta biochimica et biophysica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, functional rescue in vitro and in vivo, single lab; extends NAP1L1–HDGF axis to DDX5/β-catenin","pmids":["36148951"],"is_preprint":false},{"year":2022,"finding":"NAP1L1 interacts with HDGF (Co-IP, cytoplasmic co-localization) in ovarian cancer cells; HDGF interacts with c-Jun to induce CCND1 expression and drive cell cycle progression. HDGF overexpression in NAP1L1-knockdown cells reverses proliferation suppression.","method":"Co-IP; immunofluorescence; siRNA/shRNA knockdown; flow cytometry; cell proliferation assays; rescue experiments","journal":"BMC cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, co-localization, functional rescue, single lab; replicates NAP1L1–HDGF–c-Jun axis in another cancer type","pmids":["35351053"],"is_preprint":false},{"year":2021,"finding":"NAP1L1 binding to CHIKV nsP3 hypervariable domain (HVD) requires phosphorylation of HVD by CK2 kinase, and NAP1L1 interacts with two distinct motifs on HVD located upstream and downstream of the G3BP-binding motifs. This NAP1L1–HVD interaction has stimulatory effects on CHIKV replication in vertebrate cells.","method":"Binding assays mapping interaction to two HVD motifs; phosphorylation requirement demonstrated with CK2 inhibitors/mutants; viral replication assays; mutagenesis of HVD motifs","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — binding domain mapping, phosphorylation requirement testing, functional viral replication assays, single lab","pmids":["34076483"],"is_preprint":false},{"year":2023,"finding":"NAP1L1 is a microtubule-associated protein (MAP): it localizes in the cytosol with microtubules during interphase, binds microtubules through N-terminal (1–72 aa) and central (164–269 aa) regions, dimerizes through a long helix region (73–163 aa), and bundles microtubules in cells.","method":"Immunofluorescence microscopy of GFP/HA-tagged NAP1L1; co-localization with MTs; in vitro MT-binding assay with bacterially expressed NAP1L1 fragments and purified MTs; MT bundling assay; RNA-seq analysis of NAP1L1-depleted cells","journal":"Cytoskeleton (Hoboken, N.J.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro reconstitution with purified proteins and domain mapping, co-localization imaging, single lab","pmids":["37098731"],"is_preprint":false},{"year":2023,"finding":"MYH9 binds to NAP1L1 and recruits the deubiquitinase USP14, which prevents ubiquitination and proteasomal degradation of NAP1L1. Elevated NAP1L1 in turn binds c-Myc, activates c-Myc, and induces CCND1/CDK4 expression to promote glioma cell proliferation and temozolomide resistance.","method":"Co-IP; Western blot for ubiquitination; siRNA knockdown of MYH9 and USP14; cell proliferation and drug resistance assays; in vivo experiments","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP demonstrating MYH9–NAP1L1–USP14 complex, ubiquitination assay, functional siRNA knockdowns, single lab","pmids":["37770914"],"is_preprint":false},{"year":2023,"finding":"NAP1L1 binds YAP1 protein and influences its stability; NAP1L1 silencing promotes ubiquitination and proteasomal degradation of YAP1 in cardiac fibroblasts, thereby inhibiting fibroblast proliferation, migration, and differentiation into myofibroblasts. NAP1L1 knockout mice show reduced fibrosis after myocardial infarction.","method":"Co-IP for NAP1L1–YAP1 interaction; ubiquitination assay; siRNA/shRNA knockdown; NAP1L1 KO mice with MI model; TGF-β1 stimulation assays; Western blot","journal":"MedComm","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, KO mouse model with in vivo phenotype, single lab","pmids":["37593048"],"is_preprint":false},{"year":2025,"finding":"The somatic variant NAP1L1 p.D349E destabilizes nucleosome formation, causing cytoplasmic DNA leakage that activates the cGAS-STING innate immune pathway, leading to release of inflammatory molecules and cardiac hypertrophy. This mechanism was found in cardiomyocytes of sporadic hypertrophic cardiomyopathy patients.","method":"Next-generation sequencing identifying somatic variant; in vivo mouse model; in vitro functional analysis of nucleosome stability; cGAS-STING pathway activation assays","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo and in vitro functional analysis, pathway activation assays, single lab with multiple methods","pmids":["40169585"],"is_preprint":false},{"year":2024,"finding":"FBXW7 (E3 ubiquitin ligase) directly interacts with and ubiquitinates NAP1L1, promoting its proteasomal degradation. Reduced NAP1L1 impairs recruitment of USP14, limiting deubiquitination of HDGF, which in turn suppresses USP14-mediated p62 deubiquitination, leading to autophagy induction and enhanced cisplatin sensitivity in NPC.","method":"Co-IP; ubiquitination assay; siRNA knockdown; Western blot; autophagy flux assay; in vitro and in vivo cisplatin sensitivity assays; IHC of patient tissues","journal":"Molecular cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, functional in vitro/in vivo experiments, single lab","pmids":["40414865"],"is_preprint":false},{"year":2024,"finding":"NAP1L1 promotes DDX5 transcription by recruiting the acetyltransferase EP300 to the DDX5 promoter, leading to promoter acetylation; DDX5 then activates Wnt/β-catenin signaling by binding β-catenin, promoting endometrial cancer cell proliferation, migration, and invasion.","method":"ChIP; dual-luciferase reporter assay; Co-IP confirming NAP1L1–EP300 interaction; siRNA/shRNA knockdown; Western blot for Wnt/β-catenin; in vivo xenograft","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP, luciferase assay, Co-IP, functional in vivo model, single lab","pmids":["38953887"],"is_preprint":false},{"year":2024,"finding":"NAP1L1 does not directly bind BIRC2 (negative result from Co-IP and mass spectrometry). Instead, NAP1L1 protects BIRC2 from ubiquitination and degradation through an intermediate molecule UBR4 (E3 ubiquitin ligase); NAP1L1 knockdown promotes UBR4-mediated ubiquitin degradation of BIRC2, inhibiting HCC cell proliferation and apoptotic escape.","method":"Co-IP and mass spectrometry (no direct NAP1L1–BIRC2 interaction detected); ubiquitination assay with UBR4 depletion; siRNA knockdown; Western blot; in vitro/in vivo proliferation and apoptosis assays","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP/MS identifying intermediate protein, ubiquitination assay, functional knockdown experiments, single lab","pmids":["38538582"],"is_preprint":false},{"year":2022,"finding":"NAP1L1 is expressed in human platelets and megakaryocytes. Co-IP experiments reveal that NAP1L1 dynamically interacts with DLAT (PDC-E2), a component of the mitochondrial pyruvate dehydrogenase (PDH) complex. NAP1L1 overexpression in megakaryocytes significantly reduces proplatelet extension formation (thrombopoiesis). PDH activity is increased in platelets from septic patients paralleling NAP1L1 expression levels.","method":"Co-IP for NAP1L1–PDC-E2 interaction; NAP1L1 overexpression in megakaryocytes with proplatelet formation assay; PDH activity assay in patient platelets; RNAseq","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, functional overexpression assay with defined cellular phenotype, patient sample correlation, single lab","pmids":["36499021"],"is_preprint":false},{"year":2016,"finding":"Nap1l1 overexpression in mouse induced pluripotent stem cells (iPSCs) promotes proliferation and G2/M transition, increases cyclin B1, decreases p21 and p27, and activates AKT and ERK phosphorylation. Inhibition of AKT or ERK signaling suppresses the proliferative effects of Nap1l1 overexpression.","method":"Lentiviral overexpression and knockdown in iPSCs; MTT assay; flow cytometry for cell cycle; Western blot for cyclin B1, p21, p27, pAKT, pERK; AKT/ERK inhibitor experiments","journal":"Cellular physiology and biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — overexpression + knockdown with defined cell cycle and signaling readouts, pathway inhibitor validation, single lab","pmids":["26824453"],"is_preprint":false},{"year":2025,"finding":"The small-molecule inhibitor Z11 (identified by structure-based drug design targeting NAP1L1) interferes with NAP1L1–YAP1 interaction, promoting YAP1 ubiquitination and degradation, thereby inhibiting AKT/mTOR signaling and reducing cardiac fibroblast activation and cardiac fibrosis in TGF-β1 and MI mouse models.","method":"Structure-based drug design; in vitro TGF-β1 model; in vivo MI mouse model; Western blot for NAP1L1–YAP1 interaction disruption; ubiquitination assay; AKT/mTOR pathway analysis","journal":"European journal of pharmacology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — mechanism proposed via small-molecule interference with NAP1L1–YAP1, single lab, limited mechanistic detail in abstract","pmids":["41354299"],"is_preprint":false}],"current_model":"NAP1L1 is a histone chaperone and chromatin remodeling co-factor that enhances CSB-mediated nucleotide excision repair, regulates nucleosome assembly and gene expression (including RASSF10 via SETD1A-mediated H3K4me3 and p57(Kip2) promoter methylation), controls p53 site-specific acetylation to determine cell fate, interacts with multiple partner proteins including HDGF (promoting c-Jun/CCND1-driven proliferation in numerous cancers), YAP1 (regulating its ubiquitination and stability in cardiac fibrosis), USP14 (protecting HDGF and BIRC2 from deubiquitination), PDC-E2 (influencing mitochondrial PDH activity in platelets/megakaryocytes), and viral proteins (HCV NS5A, KSHV LANA, CHIKV nsP3 HVD), while also functioning as a microtubule-associated protein capable of bundling microtubules through defined N-terminal and central domains."},"narrative":{"mechanistic_narrative":"NAP1L1 is a histone chaperone and chromatin-acting cofactor that couples nucleosome dynamics to the control of gene expression, cell-fate decisions, and proliferation [PMID:28369616, PMID:29490266]. At the level of chromatin, it enhances CSB-mediated nucleosome remodeling by accelerating activation and translocation while suppressing CSB's non-productive DNA-binding states, thereby increasing remodeling processivity [PMID:28369616], and it directs locus-specific epigenetic marks: it promotes SETD1A-mediated H3K4 trimethylation at the RassF10 promoter to sustain neural progenitor proliferation and restrain premature neuronal differentiation [PMID:29490266], drives p57(Kip2) promoter methylation to support tumor growth via mTOR signaling [PMID:25071868], and recruits EP300 to the DDX5 promoter to activate Wnt/β-catenin signaling [PMID:38953887]. NAP1L1 also tunes p53 function by selectively modulating site-specific acetylation at Lys320 versus Lys382, biasing cells toward growth or apoptosis depending on genotoxic context [PMID:31634504]. A recurrent proliferative program across diverse cancers operates through a cytoplasmic NAP1L1–HDGF interaction in which HDGF engages c-Jun (or DDX5) to induce CCND1/CDK4/CDK6 and drive cell-cycle progression and chemoresistance [PMID:34959221, PMID:34368121, PMID:36148951]. NAP1L1 protein abundance is itself governed by ubiquitin signaling: FBXW7 ubiquitinates NAP1L1 for degradation [PMID:40414865], whereas an MYH9–USP14 axis stabilizes it [PMID:37770914], and stabilized NAP1L1 in turn shields partner proteins such as HDGF and BIRC2 (the latter through the intermediate ligase UBR4) from degradation [PMID:40414865, PMID:38538582]. Beyond chromatin, NAP1L1 functions as a microtubule-associated protein that binds and bundles microtubules through defined N-terminal and central domains and dimerizes via a central helix [PMID:37098731], stabilizes YAP1 to promote cardiac fibroblast activation and fibrosis [PMID:37593048], and is exploited by multiple viruses including HCV NS5A, KSHV LANA, and CHIKV nsP3 to modulate antiviral signaling and viral genome maintenance [PMID:28659470, PMID:27599637, PMID:34076483]. A somatic NAP1L1 p.D349E variant that destabilizes nucleosome formation triggers cytoplasmic DNA leakage and cGAS-STING activation, linking NAP1L1 dysfunction to sporadic hypertrophic cardiomyopathy [PMID:40169585].","teleology":[{"year":2014,"claim":"Established that NAP1L1 acts directly at a tumor-suppressor promoter, defining a chromatin-level mechanism for its pro-proliferative role rather than a purely structural one.","evidence":"ChIP, promoter methylation assay, and siRNA/shRNA knockdown with mTOR readouts plus orthotopic xenograft in pancreatic NEN","pmids":["25071868"],"confidence":"High","gaps":["Does not define how NAP1L1 is recruited to the p57(Kip2) promoter","Mechanistic link between NAP1L1 and the DNA methylation machinery is not resolved"]},{"year":2016,"claim":"Linked NAP1L1 abundance to mitogenic signaling, showing it drives cell-cycle progression through AKT/ERK activation.","evidence":"Lentiviral overexpression/knockdown in iPSCs with cell-cycle flow cytometry and AKT/ERK inhibitor validation","pmids":["26824453"],"confidence":"Medium","gaps":["Does not identify the direct molecular target connecting NAP1L1 to AKT/ERK","Correlative pathway readout rather than direct biochemical link"]},{"year":2016,"claim":"Showed NAP1L1 is hijacked for viral genome maintenance, positioning its nucleosome-positioning activity at a herpesviral replication origin.","evidence":"Co-IP, ChIP from depleted cells, TR plasmid replication and nucleosome positioning assays for KSHV LANA","pmids":["27599637"],"confidence":"Medium","gaps":["Single lab","Does not establish whether host chromatin uses the same recruitment logic"]},{"year":2017,"claim":"Resolved a direct biochemical function for NAP1L1 as a CSB cofactor, explaining how it enhances productive nucleosome remodeling at single-molecule resolution.","evidence":"Single-molecule real-time imaging of nucleosome remodeling and DNA-binding assays with purified CSB and NAP1L1","pmids":["28369616"],"confidence":"High","gaps":["Does not connect this in vitro activity to a specific in vivo repair or transcription outcome","Stoichiometry and binding interface with CSB not defined"]},{"year":2017,"claim":"Defined NAP1L1 as a node in antiviral innate immunity whose cytoplasmic sequestration by a viral protein blunts IRF3/RELA signaling.","evidence":"Reciprocal Co-IP mapping, immunofluorescence localization, proteasome rescue, and siRNA knockdown with IRF3 phosphorylation readouts for HCV NS5A","pmids":["28659470"],"confidence":"High","gaps":["Does not explain how nuclear NAP1L1 mechanistically supports IRF3/RELA function","Genotype-specific degradation mechanism not fully resolved"]},{"year":2018,"claim":"Demonstrated an in vivo developmental role, tying NAP1L1 to SETD1A-dependent H3K4me3 deposition that maintains neural progenitor identity.","evidence":"In utero electroporation knockdown, CRISPR KO mice, ChIP for H3K4me3, and genetic rescue by RassF10 in cortical development","pmids":["29490266"],"confidence":"High","gaps":["Does not define the physical basis of NAP1L1–SETD1A cooperation","Locus-selectivity mechanism not established"]},{"year":2019,"claim":"Revealed NAP1L1 as a context-dependent regulator of p53, selecting between growth and apoptosis through site-specific acetylation.","evidence":"siRNA knockdown with site-specific p53 acetylation, p21 and Bax readouts under normal and genotoxic conditions","pmids":["31634504"],"confidence":"Medium","gaps":["Does not identify which acetyltransferase/deacetylase NAP1L1 acts through","Single lab without reciprocal validation"]},{"year":2021,"claim":"Established a unifying pro-proliferative axis in which NAP1L1 recruits HDGF to engage c-Jun and induce cyclins, generalized across multiple cancer types.","evidence":"Co-IP, co-localization, knockdown, and HDGF/c-Jun rescue with CCND1/CDK4/CDK6 readouts in glioma, HCC, nasopharyngeal, breast and ovarian models","pmids":["34959221","34368121","34563951","34774047","35351053"],"confidence":"Medium","gaps":["Direct NAP1L1–HDGF binding interface not mapped","Why a chromatin protein operates cytoplasmically in this axis is unexplained"]},{"year":2021,"claim":"Extended the viral-cofactor role by showing phosphorylation-gated, motif-specific binding of NAP1L1 to the CHIKV nsP3 hypervariable domain.","evidence":"Domain-mapping binding assays, CK2 phosphorylation-requirement tests, and viral replication assays","pmids":["34076483"],"confidence":"Medium","gaps":["Functional consequence of the two-motif engagement not mechanistically dissected","Single lab"]},{"year":2022,"claim":"Broadened the HDGF axis to a DDX5/β-catenin output and uncovered an unexpected non-nuclear role at the mitochondrial PDH complex in platelets.","evidence":"Co-IP and rescue with β-catenin/CCND1 readouts in colon cancer; Co-IP with DLAT and proplatelet formation assay in megakaryocytes","pmids":["36148951","36499021"],"confidence":"Medium","gaps":["The PDC-E2/DLAT interaction lacks a defined biochemical mechanism","Whether NAP1L1 directly modulates PDH activity is not established"]},{"year":2023,"claim":"Reframed NAP1L1 as a bona fide microtubule-associated protein with defined binding and dimerization domains, expanding its function beyond chromatin.","evidence":"Imaging of tagged NAP1L1, in vitro MT-binding and bundling assays with bacterially expressed fragments and purified microtubules","pmids":["37098731"],"confidence":"Medium","gaps":["Physiological role of MT bundling not established","Relationship between MT and chromatin functions unresolved"]},{"year":2023,"claim":"Established NAP1L1 as a stability hub regulated by and regulating ubiquitin pathways, linking it to YAP1-driven cardiac fibrosis and a MYH9–USP14 stabilization loop.","evidence":"Co-IP, ubiquitination assays, knockdown, and KO mouse MI models for YAP1; Co-IP and ubiquitination for MYH9/USP14/c-Myc in glioma","pmids":["37593048","37770914"],"confidence":"Medium","gaps":["Direct enzymatic relationships within these complexes not fully defined","Single-lab Co-IP evidence for each interaction"]},{"year":2024,"claim":"Defined an FBXW7-driven degradation circuit and clarified NAP1L1's protective effects on partner proteins, including indirect BIRC2 stabilization via UBR4.","evidence":"Co-IP, ubiquitination assays, autophagy flux and cisplatin sensitivity assays; Co-IP/MS excluding direct BIRC2 binding and identifying UBR4 intermediate","pmids":["40414865","38538582","38953887"],"confidence":"Medium","gaps":["How a single protein integrates degradation by FBXW7/UBR4 and stabilization by USP14 is not reconciled","Tissue/context determinants of these opposing fates unknown"]},{"year":2025,"claim":"Connected NAP1L1 nucleosome-assembly function to disease, showing a destabilizing variant triggers cGAS-STING activation in hypertrophic cardiomyopathy, and provided proof-of-concept targeting of the NAP1L1–YAP1 interface.","evidence":"NGS variant identification with in vivo/in vitro nucleosome-stability and cGAS-STING assays; structure-based small-molecule (Z11) disruption of NAP1L1–YAP1 in fibrosis models","pmids":["40169585","41354299"],"confidence":"Medium","gaps":["Z11 mechanism rests on limited mechanistic detail (Low confidence)","Generality of the D349E/cGAS-STING mechanism beyond sporadic HCM not established"]},{"year":null,"claim":"It remains unresolved how NAP1L1's distinct activities — nucleosome chaperoning, microtubule bundling, ubiquitin-pathway hub, and cytoplasmic HDGF scaffolding — are coordinated within a cell and which is primary in a given tissue.","evidence":"No single study in the corpus integrates the chromatin, cytoskeletal, and proteostasis functions","pmids":[],"confidence":"Low","gaps":["No structural model linking domain architecture to multiple functions","No unifying account of nuclear versus cytoplasmic partitioning","Recruitment logic to specific promoters not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[0,1,16]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,6,14]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[13]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,3,18]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[3,5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,3,1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6,13,2]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[13]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,1,3]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[6,14,21]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[2,16]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[14,17,19]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[15,18,10]}],"complexes":[],"partners":["HDGF","YAP1","USP14","MYH9","DDX5","EP300","FBXW7","DLAT"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P55209","full_name":"Nucleosome assembly protein 1-like 1","aliases":["Histone H2A-H2B chaperone NAP1L1","NAP-1-related protein","hNRP"],"length_aa":391,"mass_kda":45.4,"function":"Histone chaperone that plays a role in the nuclear import of H2A-H2B and nucleosome assembly (PubMed:20002496, PubMed:21211722, PubMed:26841755). Also participates in several important DNA repair mechanisms: greatly enhances ERCC6-mediated chromatin remodeling which is essential for transcription-coupled nucleotide excision DNA repair (PubMed:28369616). Also stimulates homologous recombination (HR) by RAD51 and RAD54 which is essential in mitotic DNA double strand break (DSB) repair (PubMed:24798879). Plays a key role in the regulation of embryonic neurogenesis (By similarity). Promotes the proliferation of neural progenitors and inhibits neuronal differentiation during cortical development (By similarity). Regulates neurogenesis via the modulation of RASSF10; regulates RASSF10 expression by promoting SETD1A-mediated H3K4 methylation at the RASSF10 promoter (By similarity) (Microbial infection) Positively regulates Epstein-Barr virus reactivation in epithelial cells through the induction of viral BZLF1 expression (Microbial infection) Together with human herpesvirus 8 protein LANA1, assists the proper assembly of the nucleosome on the replicated viral DNA","subcellular_location":"Nucleus; Chromosome; Melanosome; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P55209/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NAP1L1","classification":"Not Classified","n_dependent_lines":12,"n_total_lines":1208,"dependency_fraction":0.009933774834437087},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"IPO5","stoichiometry":4.0},{"gene":"RPL5","stoichiometry":4.0},{"gene":"BYSL","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"H1F0","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"IPO7","stoichiometry":0.2},{"gene":"MYO1B","stoichiometry":0.2},{"gene":"MYO9B","stoichiometry":0.2},{"gene":"RBM39","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NAP1L1","total_profiled":1310},"omim":[{"mim_id":"618738","title":"TUBULIN TYROSINE LIGASE-LIKE 4; TTLL4","url":"https://www.omim.org/entry/618738"},{"mim_id":"612203","title":"NUCLEOSOME ASSEMBLY PROTEIN 1-LIKE 5; NAP1L5","url":"https://www.omim.org/entry/612203"},{"mim_id":"604714","title":"TSPY-LIKE 1; TSPYL1","url":"https://www.omim.org/entry/604714"},{"mim_id":"602820","title":"HISTONE GENE CLUSTER 3, H3 HISTONE; HIST3H3","url":"https://www.omim.org/entry/602820"},{"mim_id":"164060","title":"NUCLEOSOME ASSEMBLY PROTEIN 1-LIKE 1; NAP1L1","url":"https://www.omim.org/entry/164060"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Microtubules","reliability":"Uncertain"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NAP1L1"},"hgnc":{"alias_symbol":["NRP","NAP1","NAP1L","MGC8688","MGC23410"],"prev_symbol":[]},"alphafold":{"accession":"P55209","domains":[{"cath_id":"3.30.1120.90","chopping":"53-128_166-351","consensus_level":"medium","plddt":91.7379,"start":53,"end":351}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P55209","model_url":"https://alphafold.ebi.ac.uk/files/AF-P55209-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P55209-F1-predicted_aligned_error_v6.png","plddt_mean":79.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NAP1L1","jax_strain_url":"https://www.jax.org/strain/search?query=NAP1L1"},"sequence":{"accession":"P55209","fasta_url":"https://rest.uniprot.org/uniprotkb/P55209.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P55209/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P55209"}},"corpus_meta":[{"pmid":"30165194","id":"PMC_30165194","title":"LncRNA CDKN2B-AS1 promotes tumor growth and metastasis of human hepatocellular carcinoma by targeting let-7c-5p/NAP1L1 axis.","date":"2018","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/30165194","citation_count":137,"is_preprint":false},{"pmid":"16424981","id":"PMC_16424981","title":"The role of genetic markers--NAP1L1, MAGE-D2, and MTA1--in defining small-intestinal carcinoid neoplasia.","date":"2006","source":"Annals of surgical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/16424981","citation_count":90,"is_preprint":false},{"pmid":"30082686","id":"PMC_30082686","title":"MiR-532-5p suppresses renal cancer cell proliferation by disrupting the ETS1-mediated positive feedback loop with the KRAS-NAP1L1/P-ERK axis.","date":"2018","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/30082686","citation_count":63,"is_preprint":false},{"pmid":"9730615","id":"PMC_9730615","title":"Murine and human TSPYL genes: novel members of the TSPY-SET-NAP1L1 family.","date":"1998","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/9730615","citation_count":48,"is_preprint":false},{"pmid":"25071868","id":"PMC_25071868","title":"A mechanistic role for the chromatin modulator, NAP1L1, in pancreatic neuroendocrine neoplasm proliferation and metastases.","date":"2014","source":"Epigenetics & chromatin","url":"https://pubmed.ncbi.nlm.nih.gov/25071868","citation_count":46,"is_preprint":false},{"pmid":"29572888","id":"PMC_29572888","title":"PRDM8 exhibits antitumor activities toward hepatocellular carcinoma by targeting NAP1L1.","date":"2018","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/29572888","citation_count":39,"is_preprint":false},{"pmid":"32426045","id":"PMC_32426045","title":"Anti-vimentin, anti-TUFM, anti-NAP1L1 and anti-DPYSL2 nanobodies display cytotoxic effect and reduce glioblastoma cell migration.","date":"2020","source":"Therapeutic advances in medical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/32426045","citation_count":38,"is_preprint":false},{"pmid":"29490266","id":"PMC_29490266","title":"Nap1l1 Controls Embryonic Neural Progenitor Cell Proliferation and Differentiation in the Developing Brain.","date":"2018","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/29490266","citation_count":32,"is_preprint":false},{"pmid":"28369616","id":"PMC_28369616","title":"NAP1L1 accelerates activation and decreases pausing to enhance nucleosome remodeling by CSB.","date":"2017","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/28369616","citation_count":29,"is_preprint":false},{"pmid":"34959221","id":"PMC_34959221","title":"NAP1L1 promotes proliferation and chemoresistance in glioma by inducing CCND1/CDK4/CDK6 expression through its interaction with HDGF and activation of c-Jun.","date":"2021","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/34959221","citation_count":26,"is_preprint":false},{"pmid":"28659470","id":"PMC_28659470","title":"Hepatitis C Virus NS5A Targets Nucleosome Assembly Protein NAP1L1 To Control the Innate Cellular Response.","date":"2017","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/28659470","citation_count":25,"is_preprint":false},{"pmid":"35351053","id":"PMC_35351053","title":"NAP1L1 promotes tumor proliferation through HDGF/C-JUN signaling in ovarian cancer.","date":"2022","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/35351053","citation_count":24,"is_preprint":false},{"pmid":"38816735","id":"PMC_38816735","title":"CircDCAF8 promotes the progression of hepatocellular carcinoma through miR-217/NAP1L1 Axis, and induces angiogenesis and regorafenib resistance via exosome-mediated transfer.","date":"2024","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38816735","citation_count":23,"is_preprint":false},{"pmid":"34076483","id":"PMC_34076483","title":"NAP1L1 and NAP1L4 Binding to Hypervariable Domain of Chikungunya Virus nsP3 Protein Is Bivalent and Requires Phosphorylation.","date":"2021","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/34076483","citation_count":19,"is_preprint":false},{"pmid":"31634504","id":"PMC_31634504","title":"Nucleosome assembly proteins NAP1L1 and NAP1L4 modulate p53 acetylation to regulate cell fate.","date":"2019","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/31634504","citation_count":17,"is_preprint":false},{"pmid":"27599637","id":"PMC_27599637","title":"KSHV encoded LANA recruits Nucleosome Assembly Protein NAP1L1 for regulating viral DNA replication and transcription.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27599637","citation_count":17,"is_preprint":false},{"pmid":"26824453","id":"PMC_26824453","title":"Nucleosome Assembly Protein 1-Like 1 (Nap1l1) Regulates the Proliferation of Murine Induced Pluripotent Stem Cells.","date":"2016","source":"Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/26824453","citation_count":16,"is_preprint":false},{"pmid":"32850460","id":"PMC_32850460","title":"NAP1L1: A Novel Human Colorectal Cancer Biomarker Derived From Animal Models of Apc Inactivation.","date":"2020","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/32850460","citation_count":14,"is_preprint":false},{"pmid":"34368121","id":"PMC_34368121","title":"NAP1L1 Functions as a Tumor Promoter via Recruiting Hepatoma-Derived Growth Factor/c-Jun Signal in Hepatocellular Carcinoma.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/34368121","citation_count":14,"is_preprint":false},{"pmid":"36148951","id":"PMC_36148951","title":"NAP1L1 promotes the growth of colon cancer by activating HDGF/DDX5.","date":"2022","source":"Acta biochimica et biophysica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/36148951","citation_count":13,"is_preprint":false},{"pmid":"37770914","id":"PMC_37770914","title":"Targeting MYH9 represses USP14-mediated NAP1L1 deubiquitination and cell proliferation in glioma.","date":"2023","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/37770914","citation_count":13,"is_preprint":false},{"pmid":"34898380","id":"PMC_34898380","title":"Trametes robiniophila represses angiogenesis and tumor growth of lung cancer via strengthening let-7d-5p and targeting NAP1L1.","date":"2022","source":"Bioengineered","url":"https://pubmed.ncbi.nlm.nih.gov/34898380","citation_count":12,"is_preprint":false},{"pmid":"34563951","id":"PMC_34563951","title":"NAP1L1 targeting suppresses the proliferation of nasopharyngeal carcinoma.","date":"2021","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/34563951","citation_count":12,"is_preprint":false},{"pmid":"37593048","id":"PMC_37593048","title":"Nucleosome assembly protein 1 like 1 (NAP1L1) promotes cardiac fibrosis by inhibiting YAP1 ubiquitination and degradation.","date":"2023","source":"MedComm","url":"https://pubmed.ncbi.nlm.nih.gov/37593048","citation_count":12,"is_preprint":false},{"pmid":"34774047","id":"PMC_34774047","title":"NAP1L1 interacts with hepatoma-derived growth factor to recruit c-Jun inducing breast cancer growth.","date":"2021","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/34774047","citation_count":9,"is_preprint":false},{"pmid":"40169585","id":"PMC_40169585","title":"Somatic NAP1L1 p.D349E promotes cardiac hypertrophy through cGAS-STING-IFN signaling.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40169585","citation_count":7,"is_preprint":false},{"pmid":"38538582","id":"PMC_38538582","title":"NAP1L1 regulates BIRC2 ubiquitination modification via E3 ubiquitin ligase UBR4 and hence determines hepatocellular carcinoma progression.","date":"2024","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/38538582","citation_count":6,"is_preprint":false},{"pmid":"36499021","id":"PMC_36499021","title":"A New Role of NAP1L1 in Megakaryocytes and Human Platelets.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36499021","citation_count":5,"is_preprint":false},{"pmid":"40414865","id":"PMC_40414865","title":"NAP1L1 degradation by FBXW7 reduces the deubiquitination of HDGF-p62 signaling to stimulate autophagy and induce primary cisplatin chemosensitivity in nasopharyngeal carcinoma.","date":"2025","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40414865","citation_count":3,"is_preprint":false},{"pmid":"37098731","id":"PMC_37098731","title":"NAP1L1 is a novel microtubule-associated protein.","date":"2023","source":"Cytoskeleton (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/37098731","citation_count":2,"is_preprint":false},{"pmid":"38953887","id":"PMC_38953887","title":"NAP1L1 Promotes Endometrial Cancer Progression via EP300-Mediated DDX5 Promoter Acetylation.","date":"2024","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/38953887","citation_count":2,"is_preprint":false},{"pmid":"38988327","id":"PMC_38988327","title":"Integration of single-cell sequencing with machine learning and Mendelian randomization analysis identifies the NAP1L1 gene as a predictive biomarker for Alzheimer's disease.","date":"2024","source":"Frontiers in aging neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/38988327","citation_count":2,"is_preprint":false},{"pmid":"31987905","id":"PMC_31987905","title":"Characterization of a nap1l1 transgenic reporter in zebrafish.","date":"2020","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/31987905","citation_count":1,"is_preprint":false},{"pmid":"41354299","id":"PMC_41354299","title":"Z11, a small-molecule inhibitor of NAP1L1, alleviates cardiac fibrosis by regulating AKT/mTOR pathway.","date":"2025","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41354299","citation_count":0,"is_preprint":false},{"pmid":"42254831","id":"PMC_42254831","title":"Landscape of Immune Remodeling and NAP1L1-Driven Epithelial Reprogramming in Gastric Cancer Metastasis.","date":"2026","source":"Chronic diseases and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/42254831","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":21097,"output_tokens":6312,"usd":0.078986,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":15029,"output_tokens":5109,"usd":0.101435,"stage2_stop_reason":"end_turn"},"total_usd":0.180421,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"NAP1L1 enhances CSB-mediated nucleosome remodeling by accelerating the activation and translocation phases, and by decreasing pausing probability during translocation, thereby increasing CSB processivity. NAP1L1 also suppresses CSB's non-productive DNA-binding interactions (including gross DNA distortion).\",\n      \"method\": \"Single-molecule real-time imaging of nucleosome remodeling; DNA-binding assays with CSB and NAP1L1\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — single-molecule reconstitution with functional validation, multiple orthogonal assays (DNA binding + remodeling kinetics) in one rigorous study\",\n      \"pmids\": [\"28369616\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Nap1l1 knockdown in mouse embryos decreases neural progenitor cell (NPC) proliferation and induces premature neuronal differentiation during cortical development. Nap1l1 promotes SETD1A-mediated H3K4 trimethylation at the RassF10 promoter to upregulate RassF10 expression, and RassF10 overexpression rescues the Nap1l1 KO differentiation defect.\",\n      \"method\": \"In utero electroporation knockdown; CRISPR-Cas9 knockout mice; RNA-seq; ChIP for H3K4me3 at RassF10 promoter; rescue by RassF10 overexpression\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO mice + knockdown + ChIP + genetic rescue, multiple orthogonal methods in one study\",\n      \"pmids\": [\"29490266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"HCV NS5A interacts with NAP1L1, sequesters it in the cytoplasm blocking its nuclear translocation, and NS5A from genotype 2 (but not genotype 1) additionally targets NAP1L1 for proteasome-mediated degradation. NAP1L1 depletion reduces RELA protein levels and strongly impairs IRF3 TBK1/IKKε-mediated phosphorylation, leading to defective RIG-I and TLR3 antiviral responses.\",\n      \"method\": \"Co-IP mapping NS5A–NAP1L1 interaction; immunofluorescence for subcellular localization; proteasome inhibitor rescue; siRNA knockdown of NAP1L1 followed by IRF3 phosphorylation and RELA level assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, localization imaging, loss-of-function with defined signaling readouts, multiple orthogonal methods\",\n      \"pmids\": [\"28659470\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NAP1L1 binds directly to the p57(Kip2) promoter region (-164 to +21) and promotes its methylation; NAP1L1 silencing decreases p57(Kip2) promoter methylation, upregulates p57(Kip2) transcript and protein, inhibits mTOR pathway phosphorylation, reduces pancreatic NEN cell proliferation in vitro, and decreases tumor size in an orthotopic mouse model.\",\n      \"method\": \"siRNA/shRNA knockdown; chromatin immunoprecipitation (ChIP) at p57(Kip2) promoter; promoter methylation assay; Western blot for mTOR pathway; orthotopic xenograft model\",\n      \"journal\": \"Epigenetics & chromatin\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP demonstrating direct promoter binding, methylation assay, in vitro + in vivo KD with defined molecular readouts, multiple orthogonal methods\",\n      \"pmids\": [\"25071868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NAP1L1 knockdown decreases p53 Lys320 acetylation under normal conditions (attenuating p21 expression and facilitating cell growth), while under genotoxic stress NAP1L1 knockdown increases p53 Lys382 acetylation (enhancing proapoptotic Bax levels and facilitating cell death). Thus NAP1L1 selectively modulates site-specific p53 acetylation to determine cell fate.\",\n      \"method\": \"siRNA knockdown of NAP1L1 and NAP1L4; Western blot for acetylated p53 at Lys320 and Lys382; p21 and Bax expression assays; cell growth and apoptosis assays under normal and genotoxic stress conditions\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean siRNA KD with site-specific acetylation readouts, two conditions tested, single lab\",\n      \"pmids\": [\"31634504\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"KSHV LANA associates with NAP1L1 via its amino-terminal domain in KSHV-infected cells, recruits NAP1L1 to the terminal repeat (TR) region of the viral genome, and this interaction stimulates LANA-mediated DNA replication and TR plasmid persistence. NAP1L1 depletion reduces nucleosome positioning on the viral genome and increases transcription of viral lytic genes.\",\n      \"method\": \"Co-IP; ChIP from NAP1L1-depleted cells; TR-containing plasmid replication assay; nucleosome positioning assay; reporter assay for LANA-regulated promoters\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, ChIP, functional replication assay, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"27599637\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NAP1L1 interacts with HDGF at the protein level and they co-localize in the cytoplasm; HDGF in turn interacts with the transcription factor c-Jun, which induces expression of cell cycle promoters CCND1/CDK4/CDK6, promoting glioma cell proliferation and cisplatin chemoresistance. HDGF knockdown in NAP1L1-overexpressing cells inhibits proliferation.\",\n      \"method\": \"Co-IP; immunofluorescence co-localization; siRNA/shRNA knockdown; Western blot for CCND1/CDK4/CDK6; in vitro and in vivo proliferation assays; cisplatin sensitivity assay\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP confirming protein interaction, co-localization, functional rescue experiments, single lab\",\n      \"pmids\": [\"34959221\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NAP1L1 recruits HDGF; HDGF interacts with c-Jun transcription factor to induce CCND1 expression and stimulate HCC cell proliferation. Transfecting HDGF or c-Jun reverses the growth-suppressive effects of NAP1L1 knockdown in HCC cells.\",\n      \"method\": \"Co-IP; siRNA/shRNA knockdown; Western blot; in vitro and in vivo proliferation assays; rescue transfection of HDGF/c-Jun\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, functional rescue, in vivo xenograft, single lab; corroborates findings from other labs on same axis\",\n      \"pmids\": [\"34368121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NAP1L1 interacts with HDGF (Co-IP and co-localization in cytoplasm), and HDGF recruits c-Jun to induce CCND1 expression and drive proliferation in nasopharyngeal carcinoma. HDGF or c-Jun overexpression rescues growth suppression caused by NAP1L1 knockdown.\",\n      \"method\": \"Co-IP; immunofluorescence; siRNA/shRNA knockdown; RNA-seq; GSEA; Western blot; in vitro/in vivo proliferation assays; rescue experiments\",\n      \"journal\": \"Biomedicine & pharmacotherapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, RNA-seq pathway analysis, functional rescue, single lab; replicates NAP1L1–HDGF–c-Jun axis\",\n      \"pmids\": [\"34563951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NAP1L1 interacts with HDGF (Co-IP, confocal co-localization in cytoplasm); HDGF recruits c-Jun which induces CCND1 expression to drive breast cancer cell proliferation. HDGF overexpression rescues growth suppression from NAP1L1 knockdown.\",\n      \"method\": \"Co-IP; confocal immunofluorescence; siRNA/shRNA knockdown; MTT/Edu/colony assays; in vivo xenograft; rescue transfection\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and co-localization, functional rescue, in vivo model, single lab; independently replicates NAP1L1–HDGF–c-Jun axis\",\n      \"pmids\": [\"34774047\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NAP1L1 binds to HDGF, recruits DDX5, and induces β-catenin/CCND1 signaling to promote colon cancer cell proliferation. HDGF or DDX5 overexpression restores cell growth in NAP1L1-knockdown colon cancer cells.\",\n      \"method\": \"Co-IP; siRNA knockdown; MTT/EdU/colony assays; in vivo xenograft; rescue transfection; Western blot for β-catenin/CCND1\",\n      \"journal\": \"Acta biochimica et biophysica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, functional rescue in vitro and in vivo, single lab; extends NAP1L1–HDGF axis to DDX5/β-catenin\",\n      \"pmids\": [\"36148951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NAP1L1 interacts with HDGF (Co-IP, cytoplasmic co-localization) in ovarian cancer cells; HDGF interacts with c-Jun to induce CCND1 expression and drive cell cycle progression. HDGF overexpression in NAP1L1-knockdown cells reverses proliferation suppression.\",\n      \"method\": \"Co-IP; immunofluorescence; siRNA/shRNA knockdown; flow cytometry; cell proliferation assays; rescue experiments\",\n      \"journal\": \"BMC cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, co-localization, functional rescue, single lab; replicates NAP1L1–HDGF–c-Jun axis in another cancer type\",\n      \"pmids\": [\"35351053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NAP1L1 binding to CHIKV nsP3 hypervariable domain (HVD) requires phosphorylation of HVD by CK2 kinase, and NAP1L1 interacts with two distinct motifs on HVD located upstream and downstream of the G3BP-binding motifs. This NAP1L1–HVD interaction has stimulatory effects on CHIKV replication in vertebrate cells.\",\n      \"method\": \"Binding assays mapping interaction to two HVD motifs; phosphorylation requirement demonstrated with CK2 inhibitors/mutants; viral replication assays; mutagenesis of HVD motifs\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — binding domain mapping, phosphorylation requirement testing, functional viral replication assays, single lab\",\n      \"pmids\": [\"34076483\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NAP1L1 is a microtubule-associated protein (MAP): it localizes in the cytosol with microtubules during interphase, binds microtubules through N-terminal (1–72 aa) and central (164–269 aa) regions, dimerizes through a long helix region (73–163 aa), and bundles microtubules in cells.\",\n      \"method\": \"Immunofluorescence microscopy of GFP/HA-tagged NAP1L1; co-localization with MTs; in vitro MT-binding assay with bacterially expressed NAP1L1 fragments and purified MTs; MT bundling assay; RNA-seq analysis of NAP1L1-depleted cells\",\n      \"journal\": \"Cytoskeleton (Hoboken, N.J.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro reconstitution with purified proteins and domain mapping, co-localization imaging, single lab\",\n      \"pmids\": [\"37098731\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MYH9 binds to NAP1L1 and recruits the deubiquitinase USP14, which prevents ubiquitination and proteasomal degradation of NAP1L1. Elevated NAP1L1 in turn binds c-Myc, activates c-Myc, and induces CCND1/CDK4 expression to promote glioma cell proliferation and temozolomide resistance.\",\n      \"method\": \"Co-IP; Western blot for ubiquitination; siRNA knockdown of MYH9 and USP14; cell proliferation and drug resistance assays; in vivo experiments\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP demonstrating MYH9–NAP1L1–USP14 complex, ubiquitination assay, functional siRNA knockdowns, single lab\",\n      \"pmids\": [\"37770914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NAP1L1 binds YAP1 protein and influences its stability; NAP1L1 silencing promotes ubiquitination and proteasomal degradation of YAP1 in cardiac fibroblasts, thereby inhibiting fibroblast proliferation, migration, and differentiation into myofibroblasts. NAP1L1 knockout mice show reduced fibrosis after myocardial infarction.\",\n      \"method\": \"Co-IP for NAP1L1–YAP1 interaction; ubiquitination assay; siRNA/shRNA knockdown; NAP1L1 KO mice with MI model; TGF-β1 stimulation assays; Western blot\",\n      \"journal\": \"MedComm\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, KO mouse model with in vivo phenotype, single lab\",\n      \"pmids\": [\"37593048\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The somatic variant NAP1L1 p.D349E destabilizes nucleosome formation, causing cytoplasmic DNA leakage that activates the cGAS-STING innate immune pathway, leading to release of inflammatory molecules and cardiac hypertrophy. This mechanism was found in cardiomyocytes of sporadic hypertrophic cardiomyopathy patients.\",\n      \"method\": \"Next-generation sequencing identifying somatic variant; in vivo mouse model; in vitro functional analysis of nucleosome stability; cGAS-STING pathway activation assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo and in vitro functional analysis, pathway activation assays, single lab with multiple methods\",\n      \"pmids\": [\"40169585\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FBXW7 (E3 ubiquitin ligase) directly interacts with and ubiquitinates NAP1L1, promoting its proteasomal degradation. Reduced NAP1L1 impairs recruitment of USP14, limiting deubiquitination of HDGF, which in turn suppresses USP14-mediated p62 deubiquitination, leading to autophagy induction and enhanced cisplatin sensitivity in NPC.\",\n      \"method\": \"Co-IP; ubiquitination assay; siRNA knockdown; Western blot; autophagy flux assay; in vitro and in vivo cisplatin sensitivity assays; IHC of patient tissues\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, functional in vitro/in vivo experiments, single lab\",\n      \"pmids\": [\"40414865\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NAP1L1 promotes DDX5 transcription by recruiting the acetyltransferase EP300 to the DDX5 promoter, leading to promoter acetylation; DDX5 then activates Wnt/β-catenin signaling by binding β-catenin, promoting endometrial cancer cell proliferation, migration, and invasion.\",\n      \"method\": \"ChIP; dual-luciferase reporter assay; Co-IP confirming NAP1L1–EP300 interaction; siRNA/shRNA knockdown; Western blot for Wnt/β-catenin; in vivo xenograft\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP, luciferase assay, Co-IP, functional in vivo model, single lab\",\n      \"pmids\": [\"38953887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NAP1L1 does not directly bind BIRC2 (negative result from Co-IP and mass spectrometry). Instead, NAP1L1 protects BIRC2 from ubiquitination and degradation through an intermediate molecule UBR4 (E3 ubiquitin ligase); NAP1L1 knockdown promotes UBR4-mediated ubiquitin degradation of BIRC2, inhibiting HCC cell proliferation and apoptotic escape.\",\n      \"method\": \"Co-IP and mass spectrometry (no direct NAP1L1–BIRC2 interaction detected); ubiquitination assay with UBR4 depletion; siRNA knockdown; Western blot; in vitro/in vivo proliferation and apoptosis assays\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP/MS identifying intermediate protein, ubiquitination assay, functional knockdown experiments, single lab\",\n      \"pmids\": [\"38538582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NAP1L1 is expressed in human platelets and megakaryocytes. Co-IP experiments reveal that NAP1L1 dynamically interacts with DLAT (PDC-E2), a component of the mitochondrial pyruvate dehydrogenase (PDH) complex. NAP1L1 overexpression in megakaryocytes significantly reduces proplatelet extension formation (thrombopoiesis). PDH activity is increased in platelets from septic patients paralleling NAP1L1 expression levels.\",\n      \"method\": \"Co-IP for NAP1L1–PDC-E2 interaction; NAP1L1 overexpression in megakaryocytes with proplatelet formation assay; PDH activity assay in patient platelets; RNAseq\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, functional overexpression assay with defined cellular phenotype, patient sample correlation, single lab\",\n      \"pmids\": [\"36499021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Nap1l1 overexpression in mouse induced pluripotent stem cells (iPSCs) promotes proliferation and G2/M transition, increases cyclin B1, decreases p21 and p27, and activates AKT and ERK phosphorylation. Inhibition of AKT or ERK signaling suppresses the proliferative effects of Nap1l1 overexpression.\",\n      \"method\": \"Lentiviral overexpression and knockdown in iPSCs; MTT assay; flow cytometry for cell cycle; Western blot for cyclin B1, p21, p27, pAKT, pERK; AKT/ERK inhibitor experiments\",\n      \"journal\": \"Cellular physiology and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — overexpression + knockdown with defined cell cycle and signaling readouts, pathway inhibitor validation, single lab\",\n      \"pmids\": [\"26824453\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The small-molecule inhibitor Z11 (identified by structure-based drug design targeting NAP1L1) interferes with NAP1L1–YAP1 interaction, promoting YAP1 ubiquitination and degradation, thereby inhibiting AKT/mTOR signaling and reducing cardiac fibroblast activation and cardiac fibrosis in TGF-β1 and MI mouse models.\",\n      \"method\": \"Structure-based drug design; in vitro TGF-β1 model; in vivo MI mouse model; Western blot for NAP1L1–YAP1 interaction disruption; ubiquitination assay; AKT/mTOR pathway analysis\",\n      \"journal\": \"European journal of pharmacology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — mechanism proposed via small-molecule interference with NAP1L1–YAP1, single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"41354299\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NAP1L1 is a histone chaperone and chromatin remodeling co-factor that enhances CSB-mediated nucleotide excision repair, regulates nucleosome assembly and gene expression (including RASSF10 via SETD1A-mediated H3K4me3 and p57(Kip2) promoter methylation), controls p53 site-specific acetylation to determine cell fate, interacts with multiple partner proteins including HDGF (promoting c-Jun/CCND1-driven proliferation in numerous cancers), YAP1 (regulating its ubiquitination and stability in cardiac fibrosis), USP14 (protecting HDGF and BIRC2 from deubiquitination), PDC-E2 (influencing mitochondrial PDH activity in platelets/megakaryocytes), and viral proteins (HCV NS5A, KSHV LANA, CHIKV nsP3 HVD), while also functioning as a microtubule-associated protein capable of bundling microtubules through defined N-terminal and central domains.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NAP1L1 is a histone chaperone and chromatin-acting cofactor that couples nucleosome dynamics to the control of gene expression, cell-fate decisions, and proliferation [#0, #1]. At the level of chromatin, it enhances CSB-mediated nucleosome remodeling by accelerating activation and translocation while suppressing CSB's non-productive DNA-binding states, thereby increasing remodeling processivity [#0], and it directs locus-specific epigenetic marks: it promotes SETD1A-mediated H3K4 trimethylation at the RassF10 promoter to sustain neural progenitor proliferation and restrain premature neuronal differentiation [#1], drives p57(Kip2) promoter methylation to support tumor growth via mTOR signaling [#3], and recruits EP300 to the DDX5 promoter to activate Wnt/\\u03b2-catenin signaling [#18]. NAP1L1 also tunes p53 function by selectively modulating site-specific acetylation at Lys320 versus Lys382, biasing cells toward growth or apoptosis depending on genotoxic context [#4]. A recurrent proliferative program across diverse cancers operates through a cytoplasmic NAP1L1\\u2013HDGF interaction in which HDGF engages c-Jun (or DDX5) to induce CCND1/CDK4/CDK6 and drive cell-cycle progression and chemoresistance [#6, #7, #10]. NAP1L1 protein abundance is itself governed by ubiquitin signaling: FBXW7 ubiquitinates NAP1L1 for degradation [#17], whereas an MYH9\\u2013USP14 axis stabilizes it [#14], and stabilized NAP1L1 in turn shields partner proteins such as HDGF and BIRC2 (the latter through the intermediate ligase UBR4) from degradation [#17, #19]. Beyond chromatin, NAP1L1 functions as a microtubule-associated protein that binds and bundles microtubules through defined N-terminal and central domains and dimerizes via a central helix [#13], stabilizes YAP1 to promote cardiac fibroblast activation and fibrosis [#15], and is exploited by multiple viruses including HCV NS5A, KSHV LANA, and CHIKV nsP3 to modulate antiviral signaling and viral genome maintenance [#2, #5, #12]. A somatic NAP1L1 p.D349E variant that destabilizes nucleosome formation triggers cytoplasmic DNA leakage and cGAS-STING activation, linking NAP1L1 dysfunction to sporadic hypertrophic cardiomyopathy [#16].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established that NAP1L1 acts directly at a tumor-suppressor promoter, defining a chromatin-level mechanism for its pro-proliferative role rather than a purely structural one.\",\n      \"evidence\": \"ChIP, promoter methylation assay, and siRNA/shRNA knockdown with mTOR readouts plus orthotopic xenograft in pancreatic NEN\",\n      \"pmids\": [\"25071868\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define how NAP1L1 is recruited to the p57(Kip2) promoter\", \"Mechanistic link between NAP1L1 and the DNA methylation machinery is not resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Linked NAP1L1 abundance to mitogenic signaling, showing it drives cell-cycle progression through AKT/ERK activation.\",\n      \"evidence\": \"Lentiviral overexpression/knockdown in iPSCs with cell-cycle flow cytometry and AKT/ERK inhibitor validation\",\n      \"pmids\": [\"26824453\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify the direct molecular target connecting NAP1L1 to AKT/ERK\", \"Correlative pathway readout rather than direct biochemical link\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed NAP1L1 is hijacked for viral genome maintenance, positioning its nucleosome-positioning activity at a herpesviral replication origin.\",\n      \"evidence\": \"Co-IP, ChIP from depleted cells, TR plasmid replication and nucleosome positioning assays for KSHV LANA\",\n      \"pmids\": [\"27599637\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Does not establish whether host chromatin uses the same recruitment logic\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved a direct biochemical function for NAP1L1 as a CSB cofactor, explaining how it enhances productive nucleosome remodeling at single-molecule resolution.\",\n      \"evidence\": \"Single-molecule real-time imaging of nucleosome remodeling and DNA-binding assays with purified CSB and NAP1L1\",\n      \"pmids\": [\"28369616\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not connect this in vitro activity to a specific in vivo repair or transcription outcome\", \"Stoichiometry and binding interface with CSB not defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined NAP1L1 as a node in antiviral innate immunity whose cytoplasmic sequestration by a viral protein blunts IRF3/RELA signaling.\",\n      \"evidence\": \"Reciprocal Co-IP mapping, immunofluorescence localization, proteasome rescue, and siRNA knockdown with IRF3 phosphorylation readouts for HCV NS5A\",\n      \"pmids\": [\"28659470\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not explain how nuclear NAP1L1 mechanistically supports IRF3/RELA function\", \"Genotype-specific degradation mechanism not fully resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated an in vivo developmental role, tying NAP1L1 to SETD1A-dependent H3K4me3 deposition that maintains neural progenitor identity.\",\n      \"evidence\": \"In utero electroporation knockdown, CRISPR KO mice, ChIP for H3K4me3, and genetic rescue by RassF10 in cortical development\",\n      \"pmids\": [\"29490266\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the physical basis of NAP1L1\\u2013SETD1A cooperation\", \"Locus-selectivity mechanism not established\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed NAP1L1 as a context-dependent regulator of p53, selecting between growth and apoptosis through site-specific acetylation.\",\n      \"evidence\": \"siRNA knockdown with site-specific p53 acetylation, p21 and Bax readouts under normal and genotoxic conditions\",\n      \"pmids\": [\"31634504\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify which acetyltransferase/deacetylase NAP1L1 acts through\", \"Single lab without reciprocal validation\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established a unifying pro-proliferative axis in which NAP1L1 recruits HDGF to engage c-Jun and induce cyclins, generalized across multiple cancer types.\",\n      \"evidence\": \"Co-IP, co-localization, knockdown, and HDGF/c-Jun rescue with CCND1/CDK4/CDK6 readouts in glioma, HCC, nasopharyngeal, breast and ovarian models\",\n      \"pmids\": [\"34959221\", \"34368121\", \"34563951\", \"34774047\", \"35351053\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct NAP1L1\\u2013HDGF binding interface not mapped\", \"Why a chromatin protein operates cytoplasmically in this axis is unexplained\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended the viral-cofactor role by showing phosphorylation-gated, motif-specific binding of NAP1L1 to the CHIKV nsP3 hypervariable domain.\",\n      \"evidence\": \"Domain-mapping binding assays, CK2 phosphorylation-requirement tests, and viral replication assays\",\n      \"pmids\": [\"34076483\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the two-motif engagement not mechanistically dissected\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Broadened the HDGF axis to a DDX5/\\u03b2-catenin output and uncovered an unexpected non-nuclear role at the mitochondrial PDH complex in platelets.\",\n      \"evidence\": \"Co-IP and rescue with \\u03b2-catenin/CCND1 readouts in colon cancer; Co-IP with DLAT and proplatelet formation assay in megakaryocytes\",\n      \"pmids\": [\"36148951\", \"36499021\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The PDC-E2/DLAT interaction lacks a defined biochemical mechanism\", \"Whether NAP1L1 directly modulates PDH activity is not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Reframed NAP1L1 as a bona fide microtubule-associated protein with defined binding and dimerization domains, expanding its function beyond chromatin.\",\n      \"evidence\": \"Imaging of tagged NAP1L1, in vitro MT-binding and bundling assays with bacterially expressed fragments and purified microtubules\",\n      \"pmids\": [\"37098731\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological role of MT bundling not established\", \"Relationship between MT and chromatin functions unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established NAP1L1 as a stability hub regulated by and regulating ubiquitin pathways, linking it to YAP1-driven cardiac fibrosis and a MYH9\\u2013USP14 stabilization loop.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, knockdown, and KO mouse MI models for YAP1; Co-IP and ubiquitination for MYH9/USP14/c-Myc in glioma\",\n      \"pmids\": [\"37593048\", \"37770914\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct enzymatic relationships within these complexes not fully defined\", \"Single-lab Co-IP evidence for each interaction\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined an FBXW7-driven degradation circuit and clarified NAP1L1's protective effects on partner proteins, including indirect BIRC2 stabilization via UBR4.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, autophagy flux and cisplatin sensitivity assays; Co-IP/MS excluding direct BIRC2 binding and identifying UBR4 intermediate\",\n      \"pmids\": [\"40414865\", \"38538582\", \"38953887\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How a single protein integrates degradation by FBXW7/UBR4 and stabilization by USP14 is not reconciled\", \"Tissue/context determinants of these opposing fates unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected NAP1L1 nucleosome-assembly function to disease, showing a destabilizing variant triggers cGAS-STING activation in hypertrophic cardiomyopathy, and provided proof-of-concept targeting of the NAP1L1\\u2013YAP1 interface.\",\n      \"evidence\": \"NGS variant identification with in vivo/in vitro nucleosome-stability and cGAS-STING assays; structure-based small-molecule (Z11) disruption of NAP1L1\\u2013YAP1 in fibrosis models\",\n      \"pmids\": [\"40169585\", \"41354299\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Z11 mechanism rests on limited mechanistic detail (Low confidence)\", \"Generality of the D349E/cGAS-STING mechanism beyond sporadic HCM not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how NAP1L1's distinct activities \\u2014 nucleosome chaperoning, microtubule bundling, ubiquitin-pathway hub, and cytoplasmic HDGF scaffolding \\u2014 are coordinated within a cell and which is primary in a given tissue.\",\n      \"evidence\": \"No single study in the corpus integrates the chromatin, cytoskeletal, and proteostasis functions\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model linking domain architecture to multiple functions\", \"No unifying account of nuclear versus cytoplasmic partitioning\", \"Recruitment logic to specific promoters not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [0, 1, 16]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 6, 14]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [13]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 3, 18]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 3, 1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6, 13, 2]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [6, 14, 21]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [2, 16]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [14, 17, 19]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [15, 18, 10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"HDGF\", \"YAP1\", \"USP14\", \"MYH9\", \"DDX5\", \"EP300\", \"FBXW7\", \"DLAT\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}