{"gene":"NEIL3","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2016,"finding":"NEIL3 acts as a DNA glycosylase that unhooks interstrand cross-links (ICLs) derived from psoralen and abasic sites by cleaving one of the two N-glycosyl bonds forming the cross-link, providing a replication-coupled, incision-independent ICL repair pathway that avoids double-strand break formation. When N-glycosyl bond cleavage is blocked, repair reverts to FANCI-FANCD2-dependent incisions.","method":"Xenopus egg extract cell-free replication system; genetic epistasis (NEIL3 depletion vs. FANCI-FANCD2 depletion); biochemical ICL unhooking assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted replication-coupled repair in cell-free system with epistasis analysis and multiple orthogonal methods; independently replicated in subsequent studies","pmids":["27693351"],"is_preprint":false},{"year":2010,"finding":"Mouse Neil3 (MmuNeil3) is a functional DNA glycosylase that excises oxidized purines Sp, Gh, FapyG, and FapyA from duplex DNA, but not 8-oxoG. It preferentially acts on single-stranded DNA and bubble structures. Unlike other Fpg/Nei family members that use an N-terminal proline as nucleophile, MmuNeil3 forms a Schiff base intermediate via its N-terminal valine. In vivo, expression in an E. coli triple glycosylase mutant reduced spontaneous mutation frequency and FapyG levels.","method":"In vitro glycosylase assays on defined substrates; Schiff base trapping; in vivo complementation of E. coli fpg nei mutY triple mutant; GC-MS measurement of FapyG","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with substrate specificity profiling, mechanistic trapping, and in vivo complementation in a single rigorous study","pmids":["20185759"],"is_preprint":false},{"year":2013,"finding":"Human NEIL3 glycosylase domain (GD) efficiently excises hydantoin lesions Sp and Gh from ssDNA and dsDNA, and less efficiently removes 5OHC and 5OHU from ssDNA. Unlike NEIL1/NEIL2, which perform β,δ-elimination, NEIL3 is mainly a monofunctional glycosylase acting via β-elimination only. The V2P mutant converts NEIL3 to a bifunctional mode, demonstrating that the N-terminal Val2 amino group is critical for monofunctional activity. Residue Lys81 is essential for catalysis.","method":"In vitro glycosylase/lyase assays; site-directed mutagenesis (V2P, K81 mutants); strand incision and base excision assays on ssDNA and dsDNA substrates","journal":"DNA repair","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with active-site mutagenesis establishing catalytic mechanism, multiple substrates tested","pmids":["23755964"],"is_preprint":false},{"year":2013,"finding":"Mouse Neil3 is the only mammalian glycosylase with excision activity on thymine glycol (Tg) in quadruplex DNA, and shows strong preference for Tg in telomeric sequence context. Neil3 and NEIL1 both excise Sp and Gh from quadruplex DNA. No glycosylase tested had activity on 8-oxoG in quadruplex DNA.","method":"In vitro glycosylase assays on quadruplex DNA substrates containing Tg, 8-oxoG, Gh, or Sp; comparison across five mammalian glycosylases (NEIL1, NEIL2, mNeil3, NTH1, OGG1)","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution on defined quadruplex substrates, systematic comparison across multiple enzymes in a single study","pmids":["23926102"],"is_preprint":false},{"year":2013,"finding":"Crystal structure of mouse Neil3 glycosylase domain (MmuNeil3Δ324) at 2.0 Å resolution reveals the same overall Fpg/Nei fold but with distinct features: it lacks the αF-β9/10 loop that caps flipped-out 8-oxoG in bacterial Fpg (explaining inability to excise 8-oxoG), and it lacks void-filling residues while harboring negatively charged residues creating an unfavorable electrostatic environment for the opposite strand (explaining ssDNA preference).","method":"X-ray crystallography (2.0 Å crystal structure); structural comparison to Fpg/Nei homologs","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure with functional interpretation validated by prior biochemical data","pmids":["23313161"],"is_preprint":false},{"year":2017,"finding":"NEIL3 co-localizes with TRF2 at telomeres during S phase via interaction with TRF1; this interaction enhances NEIL3 enzymatic activity. NEIL3 binds ssDNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner. NEIL3 also interacts with APE1 and the long-patch BER proteins PCNA and FEN1. Loss of NEIL3 causes anaphase DNA bridging due to telomere dysfunction.","method":"Co-immunoprecipitation; co-localization by immunofluorescence with TRF2 and TRF1; in vitro enzymatic activity assay with TRF1; ssDNA binding assays; cell biology (anaphase bridge quantification in NEIL3 knockdown cells)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, localization with functional consequence (anaphase bridging), and in vitro enhancement of activity, multiple orthogonal methods in one study","pmids":["28854357"],"is_preprint":false},{"year":2020,"finding":"In human cells, NEIL3 is recruited to psoralen-ICLs in a rapid, PARP-dependent manner and repairs them without generating DSBs. The RUVBL1/2 complex physically interacts with NEIL3 and functions within the NEIL3 pathway for psoralen-ICL repair. TRAIP promotes recruitment of NEIL3 (but not FANCD2) to ICLs and is non-epistatic with both NEIL3 and FA pathways, placing TRAIP upstream of both. The NEIL3 and FA/BRCA pathways are non-epistatic: NEIL3 is the primary pathway and FA/BRCA is activated only when NEIL3 is absent.","method":"Co-immunoprecipitation (NEIL3–RUVBL1/2); siRNA knockdown epistasis analysis; laser-induced damage recruitment assays; DSB quantification (γH2AX); ICL sensitivity assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP for RUVBL1/2 interaction, genetic epistasis with multiple knockdowns, DSB measurement, multiple orthogonal methods","pmids":["31980815"],"is_preprint":false},{"year":2020,"finding":"The tandem GRF-type zinc finger (Zf-GRF) domain of NEIL3 provides greater affinity and specificity for ssDNA than each individual motif alone. Crystal structure of the GRF domain shows a flexible head-to-tail configuration suited for binding multiple ssDNA conformations. Functionally, the NEIL3 GRF domain inhibits (autoinhibits) glycosylase activity against both monoadducts and ICLs, distinguishing it from other GRF-ZF domains that typically enhance catalytic activity.","method":"Crystal structure of GRF domain; ssDNA binding assays; glycosylase activity assays comparing full-length vs. truncated NEIL3; ICL unhooking assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus functional biochemical assays demonstrating autoinhibition, multiple substrates tested in one study","pmids":["32878989"],"is_preprint":false},{"year":2022,"finding":"Crystal structure of the NEIL3 tandem GRF zinc-finger domain bound to DNA, combined with a structure of the NEI catalytic domain in complex with a DNA reaction intermediate, enabled construction of a model explaining how the NEI and GRF domains cooperate to recognize an ICL at a DNA replication X-structure. The GRF domain preferentially binds replication fork structures.","method":"X-ray crystallography (GRF–DNA complex; NEI domain–DNA intermediate complex); biochemical ssDNA binding assays; structural modeling of ICL recognition","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — two crystal structures with functional biochemical validation in a single study","pmids":["36155818"],"is_preprint":false},{"year":2019,"finding":"The glycosylase domain of murine NEIL3 (MmuNEIL3-GD) selectively unhooks dA-AP ICLs located at the duplex/single-strand junction of splayed duplexes modeling the leading template strand of a replication fork. NEIL3 preferentially acts on the AP residue on the leading template strand. The same strand preference applies to a 5,6-dihydrothymine monoadduct, showing it is a general feature of the glycosylase. Other BER enzymes (tested) do not unhook the dA-AP ICL.","method":"In vitro glycosylase/ICL unhooking assays on defined splayed-duplex fork substrates with site-specific dA-AP ICL or DHT monoadduct; comparison to other BER enzymes","journal":"DNA repair","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstituted in vitro with defined substrates, systematic comparison, replication-fork geometry specificity established","pmids":["31923807"],"is_preprint":false},{"year":2017,"finding":"Human NEIL3 cleaves psoralen-induced ICLs in three-stranded and four-stranded DNA substrates, generating unhooked DNA fragments containing either an abasic site or a psoralen-thymine monoadduct, without generating single-strand breaks. This activity distinguishes NEIL3 from NEIL1/Nei, which nick the DNA during unhooking.","method":"In vitro glycosylase assays on defined three-stranded and four-stranded psoralen-crosslinked DNA substrates; product analysis by gel electrophoresis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with defined substrates and comparison to NEIL1/Nei paralogs","pmids":["29234069"],"is_preprint":false},{"year":2022,"finding":"NEIL3 promotes the HR step of FA/BRCA-pathway ICL repair (for MMC and cisplatin ICLs) through its GRF zinc finger motifs, which recruit NEIL3 to DSB sites and mediate interaction with the DSB resection machinery (CtIP, MRE11-RAD50-NBS1 complex, DNA2). NEIL3 depletion reduces chromatin recruitment of resection factors, decreases end resection, and compromises HR.","method":"Co-immunoprecipitation (NEIL3 with CtIP, MRN, DNA2); chromatin fractionation; HR reporter assay; end-resection assays (RPA/BrdU ssDNA); siRNA knockdown","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, HR reporter, resection assay, and epistasis with multiple knockdowns in one study","pmids":["36351389"],"is_preprint":false},{"year":2008,"finding":"Human NEIL3 and its glycosylase domain (1-290) display AP lyase activity specific for ssDNA but not dsDNA. This activity is abolished by N-terminal deletion and by mutations at the zinc-finger motif. Expression of NEIL3 partially rescues an E. coli nth nei double mutant from hydrogen peroxide sensitivity.","method":"In vitro AP lyase assays on ssDNA/dsDNA; N-terminal deletion mutants; zinc-finger mutants; in vivo complementation of E. coli nth nei mutant","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical assays and in vivo complementation, single lab, no replication; note this study found no glycosylase activity on modified bases (negative for base excision on tested substrates)","pmids":["19170771"],"is_preprint":false},{"year":2012,"finding":"Neil3 is the main DNA glycosylase responsible for incising hydantoin lesions in ssDNA in mouse tissues (demonstrated using total cell extracts from Neil3-/- mice). Loss of Neil3 impairs self-renewal of neural stem/progenitor cells (NSPCs) and reduces proliferation of mouse embryonic fibroblasts. Neil3-/- MEFs are sensitive to paraquat (oxidative stress) and cisplatin (ICL-inducing agent).","method":"Cell extracts from Neil3-/- mice in glycosylase activity assays; neurosphere culture (self-renewal assay); MEF proliferation assays; paraquat and cisplatin sensitivity assays","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — glycosylase activity in tissue extracts plus KO cell phenotyping with multiple readouts, single lab","pmids":["23305905"],"is_preprint":false},{"year":2011,"finding":"Neil3 knockout mice show reduced numbers of proliferating neuronal progenitors in the striatum and reduced neurogenesis after hypoxia-ischemia. Neil3-deficient neural stem/progenitor cells have reduced capacity to augment neurogenesis and reduced repair of oxidative base lesions in ssDNA.","method":"Neil3-/- mouse model; hypoxia-ischemia model; cell counting of neural progenitors; in vitro neurosphere expansion; ssDNA BER activity assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined KO mouse model with cellular phenotype and DNA repair activity measurement, single lab","pmids":["22065741"],"is_preprint":false},{"year":2012,"finding":"Neil3-/- mice display learning/memory deficits and reduced anxiety-like behavior. Neural stem/progenitor cells from aged Neil3-/- mice show impaired proliferative capacity and reduced DNA repair activity (hydantoin excision in ssDNA). Hippocampal neurons in Neil3-/- mice display synaptic irregularities.","method":"Behavioral tests (learning/memory); neurosphere proliferation assays; glycosylase activity assays; synaptic morphology by electron microscopy in Neil3-/- mice","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse phenotype with multiple orthogonal readouts including DNA repair activity, single lab","pmids":["22959434"],"is_preprint":false},{"year":2005,"finding":"Mouse NEIL3 protein localizes to the nucleus as demonstrated by immunofluorescence microscopy. Neil3 mRNA is selectively expressed in hematopoietic tissues (thymus, spleen, bone marrow) and is upregulated in splenocytes after mitogen stimulation in vitro.","method":"Immunofluorescence microscopy with anti-NEIL3 antibody on recombinant mouse NEIL3; Northern blot and RT-PCR for tissue expression; mitogen stimulation of splenocytes","journal":"Journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by immunofluorescence, expression regulation confirmed by stimulation, but localization not functionally linked in same experiment","pmids":["16428305"],"is_preprint":false},{"year":2012,"finding":"hNEIL3 expression is cell cycle regulated: it is repressed in quiescent cells (G0) and induced in early S phase upon mitogenic stimulation, under control of the Ras-dependent ERK-MAP kinase pathway. This regulation parallels that of the replication protein FEN1, suggesting a replication-associated repair function.","method":"Cell cycle synchronization; Western blot and qRT-PCR for hNEIL3 protein and mRNA levels; ERK pathway inhibitor experiments; comparison to hNEIL1 and hNEIL2 expression","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological pathway inhibition establishing ERK-MAP kinase regulation, multiple time points and methods, single lab","pmids":["22365498"],"is_preprint":false},{"year":2019,"finding":"Human NEIL3 preferentially excises oxidized bases (5-hydroxyuracil, thymine glycol) from ssDNA and within open fork structures, while NEIL1 acts preferentially on dsDNA including damage upstream of the replication fork. Both enzymes act in concert at model replication fork substrates to remove oxidized bases from different structural contexts.","method":"In vitro glycosylase assays on model replication fork substrates with site-specific oxidized bases; comparison of NEIL1 and NEIL3 activity on ssDNA, dsDNA, and fork structures","journal":"Genes","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro reconstitution with defined fork substrates, single lab, single study","pmids":["31018584"],"is_preprint":false},{"year":2021,"finding":"NEIL3 co-localizes with TRF2 and repairs oxidative DNA lesions at telomeres specifically during mitosis. NEIL3-depleted HCC cells accumulate oxidative DNA lesions at telomeres, leading to telomere dysfunctional foci and 53BP1 foci. Upon oxidative DNA damage during mitosis, NEIL3 relocates to telomeres and recruits APE1, and NEIL3 (but not NEIL1 or NEIL2) is required to initiate APE1- and POLB-dependent BER at oxidized telomeres.","method":"META-FISH; immunofluorescence co-localization; NEIL3 knockdown (siRNA/shRNA) with telomere damage quantification; co-localization of NEIL3 and APE1 at telomeres; comparison to NEIL1 and NEIL2 knockdown","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional consequence, telomere-specific repair activity, comparison to paralogs, single lab","pmids":["34045188"],"is_preprint":false},{"year":2020,"finding":"The NEIL3 Zf-GRF repeat (tandem, not single GRF motif) binds APE1 (but not APE2) via protein-protein interaction. This interaction suppresses APE1 endonuclease activity on ssDNA but not dsDNA, and excess NEIL3 Zf-GRF repeat reduces DNA damage in oxidative stress in Xenopus egg extracts.","method":"Protein-protein interaction assays (pull-down); APE1 endonuclease activity assays on ssDNA/dsDNA in presence of NEIL3 Zf-GRF; COMET assays in Xenopus egg extracts","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding assay plus functional APE1 inhibition assay plus cell-free system validation, single lab","pmids":["32817342"],"is_preprint":false},{"year":2017,"finding":"NEIL3 is required for PCNA- and FEN1-dependent long-patch BER at telomeres during S/G2 phase, and loss of NEIL3 causes anaphase DNA bridging due to telomere dysfunction; NEIL3 expression peaks in late S/G2 phase.","method":"Cell cycle synchronization and Western blot for NEIL3 levels; ChIP for telomere association; siRNA knockdown with anaphase bridge quantification; co-IP of NEIL3 with PCNA and FEN1","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ChIP, cell biology phenotype, cell cycle analysis, multiple methods, single lab","pmids":["28854357"],"is_preprint":false},{"year":2018,"finding":"Mouse NEIL3 (MmuNEIL3Δ324) excises NM-Fapy-dG from ssDNA (but not dsDNA), while it cannot excise AFB1-Fapy-dG from either ssDNA or dsDNA. Product formation from ssDNA was incomplete and follows a single turnover rate of ~0.4 min-1.","method":"In vitro glycosylase assays on defined ssDNA and dsDNA oligonucleotides containing NM-Fapy-dG or AFB1-Fapy-dG; single turnover kinetics","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro reconstitution with defined substrates and kinetics, single lab, single study","pmids":["30448017"],"is_preprint":false},{"year":2017,"finding":"Loss of NEIL3 significantly increases spontaneous replication-associated DSBs and RPA recruitment, while decreasing Rad51 on nascent DNA at the replication fork, indicating that NEIL3 is required for HR-dependent repair at stalled forks. NEIL3 localizes to DSB sites during oxidative DNA damage and replication stress. NEIL3-deficient glioblastoma cells are sensitized to ATR inhibitor alone or combined with PARP1 inhibitor.","method":"NEIL3 knockdown (siRNA); γH2AX foci quantification; iPOND (isolation of proteins on nascent DNA) for Rad51 and RPA; ATR inhibitor sensitivity assays; immunofluorescence for NEIL3 at DSB sites","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — iPOND for replication-fork protein recruitment plus KO phenotype with multiple DNA damage readouts, single lab","pmids":["29348879"],"is_preprint":false},{"year":2023,"finding":"NEIL3 interacts with the 26S proteasome in a cisplatin-dependent manner (identified by proteomics) and mediates proteasomal degradation of WRNIP1, a protein involved in the early step of ICL repair. This facilitates a timely transition from lesion recognition to repair at ICL-stalled replication forks.","method":"Co-immunoprecipitation (NEIL3–26S proteasome); proteomic analysis; WRNIP1 degradation assay; gain- and loss-of-function experiments with cisplatin treatment","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and proteomic identification of 26S proteasome interaction, WRNIP1 degradation assay, single lab, single study","pmids":["36997601"],"is_preprint":false},{"year":2017,"finding":"Loss of Neil3 in mice causes increased mortality after myocardial infarction due to myocardial rupture. Neil3-/- hearts show increased proliferation of fibroblasts and myofibroblasts post-MI. Genome-wide analysis reveals changes in 5mC and 5hmC in the cardiac epigenome, particularly in genes related to proliferation and myofibroblast differentiation, suggesting NEIL3-dependent modulation of DNA methylation regulates cardiac fibroblast behavior.","method":"Neil3-/- mouse MI model; survival analysis; histology; genome-wide 5mC/5hmC profiling; fibroblast proliferation quantification","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse model with defined phenotype, genome-wide epigenome analysis, multiple cellular readouts; mechanism (methylation regulation) inferred from correlation data","pmids":["28052262"],"is_preprint":false},{"year":2022,"finding":"Neil3 deficiency in VSMCs promotes a shift towards a proliferating, lipid-accumulating, secretory macrophage-like phenotype (transdifferentiation) associated with increased Akt signaling pathway activity. NEIL3-abrogated human primary aortic VSMCs show Akt-dependent proliferation. These effects occur without changes in DNA damage levels, suggesting a non-canonical role for NEIL3 in VSMC phenotype regulation.","method":"Neil3-/- Apoe-/- mouse model; siRNA knockdown of NEIL3 in human primary aortic VSMCs; BrdU proliferation assay; Western blot for Akt phosphorylation; Akt inhibitor experiments; single-cell RNA sequencing and proteomics","journal":"Atherosclerosis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse model plus human cell knockdown with pathway inhibition, multiple orthogonal methods, single lab","pmids":["33714552"],"is_preprint":false},{"year":2022,"finding":"NEIL3 directly interacts with the EMT transcription factor TWIST1 and induces transcription of MDR1 (ABCB1) and BRAF genes through E-box promoter elements recognized by TWIST1, leading to BRAF/MEK/ERK pathway-mediated cell proliferation and drug resistance in HCC.","method":"Co-immunoprecipitation (NEIL3–TWIST1); RNA-seq; invasion/migration assays; mouse orthotopic HCC model; BRAF/MEK/ERK pathway analysis by Western blot; promoter reporter assays","journal":"The Journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct Co-IP of NEIL3–TWIST1, promoter reporter, in vivo mouse model, multiple readouts; single lab","pmids":["36181299"],"is_preprint":false},{"year":2022,"finding":"E2F1 transcriptionally activates NEIL3 expression, and NEIL3 overexpression in turn activates the cyclin D1-Rb-E2F1 pathway, forming a positive feedback loop that promotes cell proliferation and cell cycle progression in clear cell renal cell carcinoma.","method":"ChIP; luciferase reporter assay; siRNA/overexpression experiments; Western blot; cell proliferation and cell cycle assays; in vivo xenograft","journal":"DNA repair","confidence":"Low","confidence_rationale":"Tier 3 / Weak — ChIP and reporter assay establish transcriptional regulation, but mechanistic link between NEIL3 and cyclin D1-Rb-E2F1 relies on Western blot and overexpression without direct biochemical interaction evidence; single lab","pmids":["37992567"],"is_preprint":false},{"year":2022,"finding":"SNHG3 increases E2F1 binding to the NEIL3 promoter region, thereby activating NEIL3 transcription in hepatocellular carcinoma cells. NEIL3 participates in SNHG3-mediated regulation of HCC cell cycle, apoptosis, and proliferation (rescue experiments).","method":"ChIP assay (E2F1 binding to NEIL3 promoter); luciferase reporter; siRNA knockdown of SNHG3; rescue experiments with NEIL3 overexpression; CCK-8; flow cytometry","journal":"Immunogenetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — ChIP establishes E2F1–NEIL3 promoter binding, rescue experiments link NEIL3 to SNHG3 pathway, but molecular mechanism of NEIL3 in proliferation not defined; single lab","pmids":["36114381"],"is_preprint":false},{"year":2025,"finding":"NEIL3 deficiency leads to reduced PV+ GABAergic interneurons, impaired perineuronal net (PNN) integrity, altered hippocampal oscillatory dynamics (increased beta and low gamma power; reduced high gamma and ripple activity), and distinct effects on contextual vs. trace fear memory. Transcriptomic analysis reveals dysregulation of glutamatergic/GABAergic signaling genes, including Gabra2 downregulation potentially driven by changes in promoter DNA methylation.","method":"Neil3-/- mouse model; immunofluorescence (PV+ interneuron counting); PNN staining; in vivo electrophysiology (hippocampal oscillations); fear conditioning behavioral paradigms; RNA sequencing; bisulfite sequencing (DNA methylation)","journal":"Progress in neurobiology","confidence":"Low","confidence_rationale":"Tier 2 / Weak — multiple readouts in KO model but mechanism linking NEIL3 DNA repair to PV+ interneuron regulation is not directly established biochemically; single lab, no replication","pmids":["41015225"],"is_preprint":false},{"year":2025,"finding":"NEIL3 deficiency impairs adult hippocampal neurogenesis and behavioral pattern separation through altered transcriptional regulation of the Wnt signaling pathway, not through decreased genomic integrity. NEIL3-deficient adult-born neurons show reduced mature-like membrane properties.","method":"Neil3-/- mouse model; neurosphere proliferation and differentiation assays; behavioral pattern separation tests; electrophysiology of adult-born neurons; RNA sequencing; Wnt pathway inhibitor experiments","journal":"Cellular and molecular life sciences : CMLS","confidence":"Low","confidence_rationale":"Tier 2 / Weak — KO model with multiple phenotypic readouts and pathway analysis, but direct molecular link between NEIL3 and Wnt pathway regulation not established biochemically; single lab","pmids":["40035863"],"is_preprint":false}],"current_model":"NEIL3 is a DNA glycosylase of the Fpg/Nei superfamily that initiates base excision repair by excising oxidized purine and pyrimidine lesions (particularly hydantoins Sp and Gh, FapyG, FapyA, and thymine glycol) with a marked preference for single-stranded DNA and DNA fork structures, using its N-terminal valine as the catalytic nucleophile to form a Schiff base intermediate and acting primarily as a monofunctional glycosylase (β-elimination only); its C-terminal tandem GRF zinc-finger domain binds ssDNA with high affinity, autoinhibits glycosylase activity, and mediates interaction with APE1 to suppress aberrant ssDNA cleavage; during S phase NEIL3 is recruited via TRAIP-dependent CMG helicase ubiquitylation and through interaction with TRF1 to repair oxidative lesions at telomeres and to unhook replication fork-stalled interstrand cross-links (psoralen- and abasic site-derived) by direct N-glycosyl bond cleavage without generating double-strand breaks—the preferred ICL repair route that acts upstream of the FANCI-FANCD2/Fanconi anemia pathway; additionally, NEIL3 promotes the homologous recombination step of FA-pathway repair via GRF-mediated interaction with CtIP, MRN, and DNA2, and cooperates with RUVBL1/2 in psoralen-ICL repair; beyond canonical BER, NEIL3 interacts with TWIST1 to activate EMT gene programs and has non-canonical roles in regulating cardiac fibroblast proliferation, vascular smooth muscle cell phenotype (via Akt signaling), and adult hippocampal neurogenesis (partly through Wnt signaling)."},"narrative":{"mechanistic_narrative":"NEIL3 is a DNA glycosylase of the Fpg/Nei superfamily that initiates base excision repair of oxidized DNA lesions, with a marked preference for single-stranded DNA and replication-fork structures [PMID:20185759, PMID:31018584]. It excises oxidized purine hydantoins (spiroiminodihydantoin, guanidinohydantoin), FapyG, FapyA, and thymine glycol, but not 8-oxoG [PMID:20185759, PMID:23755964], and uniquely among mammalian glycosylases removes thymine glycol from quadruplex/telomeric DNA [PMID:23926102]. Unlike its paralogs NEIL1/NEIL2, NEIL3 acts as a monofunctional glycosylase (β-elimination only) using its N-terminal valine rather than proline as the catalytic nucleophile to form a Schiff base intermediate; the V2P mutation converts it to a bifunctional enzyme and Lys81 is essential for catalysis [PMID:20185759, PMID:23755964]. Structural studies of the mouse glycosylase domain explain both its inability to excise 8-oxoG (loss of the αF-β9/10 capping loop) and its ssDNA preference (an unfavorable electrostatic environment for the opposite strand) [PMID:23313161]. Its C-terminal tandem GRF zinc-finger domain binds ssDNA and replication-fork structures with high affinity, autoinhibits glycosylase activity, and mediates an interaction with APE1 that suppresses aberrant APE1 endonuclease cleavage of ssDNA [PMID:32878989, PMID:36155818, PMID:32817342]. NEIL3 defines a replication-coupled, incision-independent pathway for unhooking interstrand cross-links: it cleaves one of the two N-glycosyl bonds of psoralen- and abasic-site-derived ICLs without generating double-strand breaks, acting upstream of and as the preferred route over the FANCI-FANCD2/Fanconi anemia pathway, which is engaged only when N-glycosyl cleavage fails [PMID:27693351, PMID:31923807, PMID:29234069]. During S/G2 phase NEIL3 is recruited to telomeres through interaction with TRF1 and to ICLs through PARP- and TRAIP-dependent signaling, cooperating with RUVBL1/2, PCNA, and FEN1 to repair oxidative and cross-link damage and prevent telomere dysfunction and anaphase bridging [PMID:28854357, PMID:31980815, PMID:34045188]. Through its GRF domain NEIL3 also promotes the homologous-recombination step of FA/BRCA ICL repair by recruiting the resection machinery CtIP, MRN, and DNA2 [PMID:36351389, PMID:29348879]. Beyond DNA repair, NEIL3 interacts with the EMT factor TWIST1 to drive proliferation and drug-resistance gene programs in cancer, and its expression is cell-cycle regulated via the Ras-ERK pathway and transcriptionally controlled by E2F1 [PMID:22365498, PMID:36181299, PMID:37992567]. Knockout mouse studies link NEIL3 to neural stem/progenitor self-renewal, hippocampal neurogenesis, and cardiac fibroblast regulation [PMID:23305905, PMID:22065741, PMID:28052262].","teleology":[{"year":2010,"claim":"Establishing NEIL3 as a bona fide glycosylase answered whether this Fpg/Nei member had catalytic activity and defined its unusual substrate range and chemistry.","evidence":"In vitro glycosylase assays, Schiff-base trapping, and E. coli triple-mutant complementation with mouse Neil3","pmids":["20185759"],"confidence":"High","gaps":["Did not resolve the structural basis for ssDNA preference","Human enzyme catalytic mode not yet defined"]},{"year":2013,"claim":"Defining the catalytic mechanism and structure clarified why NEIL3 is monofunctional and ssDNA-selective and cannot process 8-oxoG.","evidence":"Active-site mutagenesis (V2P, K81) and a 2.0 Å crystal structure of the mouse glycosylase domain with substrate profiling including quadruplex DNA","pmids":["23755964","23313161","23926102"],"confidence":"High","gaps":["Did not address how the C-terminal GRF domain regulates catalysis","In-cell substrate spectrum not established"]},{"year":2008,"claim":"An early biochemical characterization established AP lyase activity specific for ssDNA and the requirement of the N-terminus and zinc-finger motif.","evidence":"In vitro AP lyase assays with deletion/zinc-finger mutants and E. coli complementation of human NEIL3","pmids":["19170771"],"confidence":"Medium","gaps":["No glycosylase activity on modified bases detected in this study","Single lab, no replication"]},{"year":2016,"claim":"Discovery of incision-independent ICL unhooking answered how cross-links can be repaired without double-strand breaks and placed NEIL3 upstream of the Fanconi anemia pathway.","evidence":"Xenopus egg-extract replication-coupled repair with genetic epistasis against FANCI-FANCD2 and biochemical unhooking assays","pmids":["27693351"],"confidence":"High","gaps":["Recruitment signal to the fork not yet defined","Structural basis of ICL recognition unresolved"]},{"year":2017,"claim":"Identifying telomeric recruitment and BER partner interactions established a cell-cycle-coupled role at telomeres and connected NEIL3 to long-patch BER.","evidence":"Co-IP and co-localization with TRF1/TRF2, in vitro activity enhancement by TRF1, anaphase-bridge quantification in knockdown cells; psoralen-ICL cleavage in multi-stranded substrates","pmids":["28854357","29234069"],"confidence":"High","gaps":["How TRF1 enhances enzymatic activity mechanistically unknown","Telomere vs. genome-wide division of labor not quantified"]},{"year":2019,"claim":"Defining replication-fork geometry preference showed that NEIL3 acts on lesions on the leading template strand and shares fork substrates with NEIL1.","evidence":"In vitro unhooking and glycosylase assays on splayed-duplex and model fork substrates with site-specific dA-AP ICLs, DHT, and oxidized bases","pmids":["31923807","31018584"],"confidence":"High","gaps":["Single-lab fork substrate models","Coordination with NEIL1 in cells not demonstrated"]},{"year":2020,"claim":"Characterizing the GRF domain and its partners answered how NEIL3 binds ssDNA, restrains its own activity, and controls APE1 during repair.","evidence":"Crystal structure of the tandem GRF domain, ssDNA-binding and autoinhibition assays, APE1/RUVBL1-2 pull-downs and activity assays, PARP/TRAIP epistasis in human cells","pmids":["32878989","32817342","31980815"],"confidence":"High","gaps":["How autoinhibition is relieved at the lesion is unclear","TRAIP-to-NEIL3 recruitment signal not biochemically defined"]},{"year":2022,"claim":"Structural modeling of GRF-DNA and catalytic-domain-intermediate complexes provided a coherent model for how the two domains cooperate to recognize an ICL at a replication X-structure.","evidence":"Two crystal structures (GRF-DNA; NEI domain-DNA intermediate) with biochemical ssDNA-binding validation","pmids":["36155818"],"confidence":"High","gaps":["Full-length enzyme-fork complex not solved","Dynamics of domain handoff not captured"]},{"year":2022,"claim":"Defining a GRF-dependent role in HR resection answered how NEIL3 also contributes to the Fanconi-anemia/BRCA branch of ICL repair when used for MMC and cisplatin lesions.","evidence":"Co-IP with CtIP/MRN/DNA2, chromatin fractionation, end-resection and HR reporter assays with knockdowns; complemented by iPOND-based fork data","pmids":["36351389","29348879"],"confidence":"Medium","gaps":["Whether resection role requires glycosylase activity is unresolved","Direct vs. bridging interactions with resection factors not distinguished"]},{"year":2021,"claim":"Telomere-specific oxidative repair during mitosis established NEIL3 as the dedicated initiator of APE1/POLB BER at oxidized telomeres, distinct from NEIL1/NEIL2.","evidence":"META-FISH, co-localization with TRF2 and APE1, telomere-damage quantification with paralog comparison in HCC cells","pmids":["34045188"],"confidence":"Medium","gaps":["Single cancer-cell context","Mechanism of mitosis-specific recruitment not defined"]},{"year":2023,"claim":"Identifying proteasome-dependent WRNIP1 degradation suggested NEIL3 also coordinates the lesion-recognition-to-repair transition at ICL-stalled forks.","evidence":"Proteomics, Co-IP of NEIL3 with 26S proteasome, and WRNIP1 degradation assays under cisplatin","pmids":["36997601"],"confidence":"Medium","gaps":["Whether NEIL3 directly targets WRNIP1 to the proteasome unclear","Single lab, single study"]},{"year":2022,"claim":"Linking NEIL3 to TWIST1 and to E2F1 transcriptional circuits revealed non-canonical, repair-independent roles in cancer proliferation and drug resistance.","evidence":"Co-IP of NEIL3-TWIST1, promoter reporters, RNA-seq and orthotopic models in HCC; ChIP/reporter for E2F1-NEIL3 feedback in renal carcinoma","pmids":["36181299","28052262"],"confidence":"Medium","gaps":["Whether the glycosylase activity is required for transcriptional functions unknown","Direct vs. indirect TWIST1 cooperation not fully resolved"]},{"year":2012,"claim":"Cell-cycle and pathway regulation of NEIL3 expression connected it to replication-associated repair, paralleling FEN1.","evidence":"Cell-cycle synchronization, ERK-pathway inhibition, and qRT-PCR/Western analysis of human NEIL3","pmids":["22365498"],"confidence":"Medium","gaps":["Direct transcription factors at the promoter not all identified here","Link to repair function correlative"]},{"year":2012,"claim":"Knockout mouse phenotyping established physiological roles of NEIL3 in neural stem-cell self-renewal, neurogenesis, and behavior, and confirmed it as the principal ssDNA hydantoin glycosylase in tissue.","evidence":"Neil3-/- mice with neurosphere, MEF proliferation, behavioral, electron-microscopy, hypoxia-ischemia, and tissue-extract glycosylase assays","pmids":["23305905","22065741","22959434"],"confidence":"Medium","gaps":["Whether neural phenotypes require glycosylase activity not established","Causal repair-to-phenotype link inferred"]},{"year":2025,"claim":"Recent knockout studies attributed neural and behavioral phenotypes to transcriptional/epigenetic rather than genomic-integrity mechanisms, including Wnt-pathway and DNA-methylation effects.","evidence":"Neil3-/- mice with electrophysiology, fear conditioning, neurosphere assays, RNA-seq, bisulfite sequencing, and Wnt-inhibitor experiments","pmids":["41015225","40035863"],"confidence":"Low","gaps":["Direct biochemical link between NEIL3 and Wnt/methylation not established","Single-lab models without independent replication"]},{"year":2022,"claim":"Cardiovascular knockout studies indicated non-canonical roles for NEIL3 in cardiac fibroblast and vascular smooth muscle cell behavior, possibly via epigenetic and Akt signaling.","evidence":"Neil3-/- mouse MI and Apoe-/- models, human VSMC knockdown, 5mC/5hmC profiling, Akt phosphorylation and inhibitor assays, scRNA-seq","pmids":["28052262","33714552"],"confidence":"Medium","gaps":["Mechanism connecting NEIL3 to DNA methylation and Akt is correlative","Effects reported without changes in DNA damage levels"]},{"year":null,"claim":"How NEIL3's canonical glycosylase chemistry relates mechanistically to its repair-independent transcriptional, epigenetic, and signaling roles remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No experiment separates catalytic-dependent from catalytic-independent functions in vivo","No structure of the full-length enzyme engaging a replication fork","No direct demonstration that NEIL3 enzymatically alters DNA methylation marks"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140097","term_label":"catalytic activity, acting on DNA","supporting_discovery_ids":[0,1,2,3,9,10,18,22]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[7,8,12,20]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,9,10,12]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[27]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[16]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[5,19,21]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,6,11,23]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[5,9,18,21]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[17,21]}],"complexes":[],"partners":["TRF1","APE1","PCNA","FEN1","RUVBL1","CTIP","DNA2","TWIST1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8TAT5","full_name":"Endonuclease 8-like 3","aliases":["DNA glycosylase FPG2","DNA glycosylase/AP lyase Neil3","Endonuclease VIII-like 3","Nei-like protein 3"],"length_aa":605,"mass_kda":67.8,"function":"DNA glycosylase which prefers single-stranded DNA (ssDNA), or partially ssDNA structures such as bubble and fork structures, to double-stranded DNA (dsDNA) (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). Mediates interstrand cross-link repair in response to replication stress: acts by mediating DNA glycosylase activity, cleaving one of the two N-glycosyl bonds comprising the interstrand cross-link, which avoids the formation of a double-strand break but generates an abasic site that is bypassed by translesion synthesis polymerases (By similarity). In vitro, displays strong glycosylase activity towards the hydantoin lesions spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh) in both ssDNA and dsDNA; also recognizes FapyA, FapyG, 5-OHU, 5-OHC, 5-OHMH, Tg and 8-oxoA lesions in ssDNA (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). No activity on 8-oxoG detected (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). Also shows weak DNA-(apurinic or apyrimidinic site) lyase activity (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964). In vivo, appears to be the primary enzyme involved in removing Sp and Gh from ssDNA in neonatal tissues (PubMed:12433996, PubMed:19170771, PubMed:22569481, PubMed:23755964)","subcellular_location":"Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q8TAT5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NEIL3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"FKBP5","stoichiometry":0.2},{"gene":"PTGES3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NEIL3","total_profiled":1310},"omim":[{"mim_id":"608934","title":"ENDONUCLEASE VIII-LIKE 3; NEIL3","url":"https://www.omim.org/entry/608934"},{"mim_id":"605958","title":"TRAF-INTERACTING PROTEIN; TRAIP","url":"https://www.omim.org/entry/605958"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"bone marrow","ntpm":6.3},{"tissue":"lymphoid tissue","ntpm":22.0}],"url":"https://www.proteinatlas.org/search/NEIL3"},"hgnc":{"alias_symbol":["FLJ10858","hFPG2","FPG2","hNEI3","ZGRF3"],"prev_symbol":[]},"alphafold":{"accession":"Q8TAT5","domains":[{"cath_id":"3.20.190.10","chopping":"5-43_60-151","consensus_level":"high","plddt":86.4416,"start":5,"end":151},{"cath_id":"1.10.8.50","chopping":"153-292","consensus_level":"high","plddt":93.6271,"start":153,"end":292},{"cath_id":"-","chopping":"519-593","consensus_level":"high","plddt":83.2012,"start":519,"end":593}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TAT5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TAT5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TAT5-F1-predicted_aligned_error_v6.png","plddt_mean":69.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NEIL3","jax_strain_url":"https://www.jax.org/strain/search?query=NEIL3"},"sequence":{"accession":"Q8TAT5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8TAT5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8TAT5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TAT5"}},"corpus_meta":[{"pmid":"27693351","id":"PMC_27693351","title":"Replication-Dependent 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from the architecture of NEIL3 DNA binding domains to the X-structure model.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/36155818","citation_count":12,"is_preprint":false},{"pmid":"27167163","id":"PMC_27167163","title":"Single nucleotide polymorphisms in the REG-CTNNA2 region of chromosome 2 and NEIL3 associated with impulsivity in a Native American sample.","date":"2016","source":"Genes, brain, and behavior","url":"https://pubmed.ncbi.nlm.nih.gov/27167163","citation_count":12,"is_preprint":false},{"pmid":"37121465","id":"PMC_37121465","title":"Transcriptional factor MAZ promotes cisplatin-induced DNA damage repair in lung adenocarcinoma by regulating NEIL3.","date":"2023","source":"Pulmonary pharmacology & therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/37121465","citation_count":11,"is_preprint":false},{"pmid":"36351389","id":"PMC_36351389","title":"NEIL3 contributes to the Fanconi anemia/BRCA pathway by promoting the downstream double-strand break repair step.","date":"2022","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36351389","citation_count":11,"is_preprint":false},{"pmid":"30311321","id":"PMC_30311321","title":"Identification of retinal homeobox (rax) gene-dependent genes by a microarray approach: The DNA endoglycosylase neil3 is a major downstream component of the rax genetic pathway.","date":"2018","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/30311321","citation_count":9,"is_preprint":false},{"pmid":"35079641","id":"PMC_35079641","title":"NEIL3-deficient bone marrow displays decreased hematopoietic capacity and reduced telomere length.","date":"2022","source":"Biochemistry and biophysics reports","url":"https://pubmed.ncbi.nlm.nih.gov/35079641","citation_count":8,"is_preprint":false},{"pmid":"34988395","id":"PMC_34988395","title":"DNA repair enzyme NEIL3 enables a stable neural representation of space by shaping transcription in hippocampal neurons.","date":"2021","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/34988395","citation_count":8,"is_preprint":false},{"pmid":"39342941","id":"PMC_39342941","title":"NEIL3 Upregulated by TFAP2A Promotes M2 Polarization of Macrophages in Liver Cancer via the Mediation of Glutamine Metabolism.","date":"2024","source":"Digestion","url":"https://pubmed.ncbi.nlm.nih.gov/39342941","citation_count":8,"is_preprint":false},{"pmid":"36997601","id":"PMC_36997601","title":"NEIL3-mediated proteasomal degradation facilitates the repair of cisplatin-induced DNA damage in human cells.","date":"2023","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/36997601","citation_count":7,"is_preprint":false},{"pmid":"36395955","id":"PMC_36395955","title":"Age- and sex-dependent effects of DNA glycosylase Neil3 on amyloid pathology, adult neurogenesis, and memory in a mouse model of Alzheimer's disease.","date":"2022","source":"Free radical biology & medicine","url":"https://pubmed.ncbi.nlm.nih.gov/36395955","citation_count":6,"is_preprint":false},{"pmid":"34611194","id":"PMC_34611194","title":"NEIL3-deficiency increases gut permeability and contributes to a pro-atherogenic metabolic phenotype.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/34611194","citation_count":5,"is_preprint":false},{"pmid":"38198604","id":"PMC_38198604","title":"Novel Processes Associated with the Repair of Interstrand Cross-Links Derived from Abasic Sites in Duplex DNA: Roles for the Base Excision Repair Glycosylase NEIL3 and the SRAP Protein HMCES.","date":"2024","source":"Chemical research in toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/38198604","citation_count":5,"is_preprint":false},{"pmid":"40035863","id":"PMC_40035863","title":"NEIL3 influences adult neurogenesis and behavioral pattern separation via WNT signaling.","date":"2025","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/40035863","citation_count":5,"is_preprint":false},{"pmid":"37437684","id":"PMC_37437684","title":"NEIL3 promoter G-quadruplex with oxidatively modified bases shows magnesium-dependent folding that stalls polymerase bypass.","date":"2023","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/37437684","citation_count":5,"is_preprint":false},{"pmid":"36546838","id":"PMC_36546838","title":"WT1 regulates expression of DNA repair gene Neil3 during nephrogenesis.","date":"2022","source":"American journal of physiology. Renal physiology","url":"https://pubmed.ncbi.nlm.nih.gov/36546838","citation_count":4,"is_preprint":false},{"pmid":"36612106","id":"PMC_36612106","title":"Pan-Cancer Landscape of NEIL3 in Tumor Microenvironment: A Promising Predictor for Chemotherapy and Immunotherapy.","date":"2022","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/36612106","citation_count":4,"is_preprint":false},{"pmid":"37992567","id":"PMC_37992567","title":"NEIL3 promotes cell proliferation of ccRCC via the cyclin D1-Rb-E2F1 feedback loop regulation.","date":"2023","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/37992567","citation_count":2,"is_preprint":false},{"pmid":"40447877","id":"PMC_40447877","title":"NEIL3 promotes the carcinogenesis of prostate cancer by activating PI3K/Akt/mTOR signaling.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40447877","citation_count":1,"is_preprint":false},{"pmid":"40263742","id":"PMC_40263742","title":"NEIL3 Deficiency Enhances HCC Cell Sensitivity to Oxaliplatin by Inhibiting the Fanconi Anaemia Pathway.","date":"2025","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/40263742","citation_count":0,"is_preprint":false},{"pmid":"39910812","id":"PMC_39910812","title":"NEIL3 and TOP2A as key drivers of esophageal cancer through WNT signaling.","date":"2025","source":"Biomolecules & biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/39910812","citation_count":0,"is_preprint":false},{"pmid":"41015225","id":"PMC_41015225","title":"NEIL3 shapes hippocampal network dynamics and fear memory through modulation of PV+ interneurons.","date":"2025","source":"Progress in neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/41015225","citation_count":0,"is_preprint":false},{"pmid":"40777817","id":"PMC_40777817","title":"FOXM1 transcriptionally activates NEIL3 to inhibit ferroptosis in lung adenocarcinoma cells.","date":"2025","source":"Journal of clinical biochemistry and nutrition","url":"https://pubmed.ncbi.nlm.nih.gov/40777817","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":32706,"output_tokens":8912,"usd":0.115899,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":19157,"output_tokens":5430,"usd":0.115767,"stage2_stop_reason":"end_turn"},"total_usd":0.231666,"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\": 2016,\n      \"finding\": \"NEIL3 acts as a DNA glycosylase that unhooks interstrand cross-links (ICLs) derived from psoralen and abasic sites by cleaving one of the two N-glycosyl bonds forming the cross-link, providing a replication-coupled, incision-independent ICL repair pathway that avoids double-strand break formation. When N-glycosyl bond cleavage is blocked, repair reverts to FANCI-FANCD2-dependent incisions.\",\n      \"method\": \"Xenopus egg extract cell-free replication system; genetic epistasis (NEIL3 depletion vs. FANCI-FANCD2 depletion); biochemical ICL unhooking assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted replication-coupled repair in cell-free system with epistasis analysis and multiple orthogonal methods; independently replicated in subsequent studies\",\n      \"pmids\": [\"27693351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Mouse Neil3 (MmuNeil3) is a functional DNA glycosylase that excises oxidized purines Sp, Gh, FapyG, and FapyA from duplex DNA, but not 8-oxoG. It preferentially acts on single-stranded DNA and bubble structures. Unlike other Fpg/Nei family members that use an N-terminal proline as nucleophile, MmuNeil3 forms a Schiff base intermediate via its N-terminal valine. In vivo, expression in an E. coli triple glycosylase mutant reduced spontaneous mutation frequency and FapyG levels.\",\n      \"method\": \"In vitro glycosylase assays on defined substrates; Schiff base trapping; in vivo complementation of E. coli fpg nei mutY triple mutant; GC-MS measurement of FapyG\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with substrate specificity profiling, mechanistic trapping, and in vivo complementation in a single rigorous study\",\n      \"pmids\": [\"20185759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Human NEIL3 glycosylase domain (GD) efficiently excises hydantoin lesions Sp and Gh from ssDNA and dsDNA, and less efficiently removes 5OHC and 5OHU from ssDNA. Unlike NEIL1/NEIL2, which perform β,δ-elimination, NEIL3 is mainly a monofunctional glycosylase acting via β-elimination only. The V2P mutant converts NEIL3 to a bifunctional mode, demonstrating that the N-terminal Val2 amino group is critical for monofunctional activity. Residue Lys81 is essential for catalysis.\",\n      \"method\": \"In vitro glycosylase/lyase assays; site-directed mutagenesis (V2P, K81 mutants); strand incision and base excision assays on ssDNA and dsDNA substrates\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with active-site mutagenesis establishing catalytic mechanism, multiple substrates tested\",\n      \"pmids\": [\"23755964\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Mouse Neil3 is the only mammalian glycosylase with excision activity on thymine glycol (Tg) in quadruplex DNA, and shows strong preference for Tg in telomeric sequence context. Neil3 and NEIL1 both excise Sp and Gh from quadruplex DNA. No glycosylase tested had activity on 8-oxoG in quadruplex DNA.\",\n      \"method\": \"In vitro glycosylase assays on quadruplex DNA substrates containing Tg, 8-oxoG, Gh, or Sp; comparison across five mammalian glycosylases (NEIL1, NEIL2, mNeil3, NTH1, OGG1)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution on defined quadruplex substrates, systematic comparison across multiple enzymes in a single study\",\n      \"pmids\": [\"23926102\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Crystal structure of mouse Neil3 glycosylase domain (MmuNeil3Δ324) at 2.0 Å resolution reveals the same overall Fpg/Nei fold but with distinct features: it lacks the αF-β9/10 loop that caps flipped-out 8-oxoG in bacterial Fpg (explaining inability to excise 8-oxoG), and it lacks void-filling residues while harboring negatively charged residues creating an unfavorable electrostatic environment for the opposite strand (explaining ssDNA preference).\",\n      \"method\": \"X-ray crystallography (2.0 Å crystal structure); structural comparison to Fpg/Nei homologs\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure with functional interpretation validated by prior biochemical data\",\n      \"pmids\": [\"23313161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NEIL3 co-localizes with TRF2 at telomeres during S phase via interaction with TRF1; this interaction enhances NEIL3 enzymatic activity. NEIL3 binds ssDNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner. NEIL3 also interacts with APE1 and the long-patch BER proteins PCNA and FEN1. Loss of NEIL3 causes anaphase DNA bridging due to telomere dysfunction.\",\n      \"method\": \"Co-immunoprecipitation; co-localization by immunofluorescence with TRF2 and TRF1; in vitro enzymatic activity assay with TRF1; ssDNA binding assays; cell biology (anaphase bridge quantification in NEIL3 knockdown cells)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, localization with functional consequence (anaphase bridging), and in vitro enhancement of activity, multiple orthogonal methods in one study\",\n      \"pmids\": [\"28854357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In human cells, NEIL3 is recruited to psoralen-ICLs in a rapid, PARP-dependent manner and repairs them without generating DSBs. The RUVBL1/2 complex physically interacts with NEIL3 and functions within the NEIL3 pathway for psoralen-ICL repair. TRAIP promotes recruitment of NEIL3 (but not FANCD2) to ICLs and is non-epistatic with both NEIL3 and FA pathways, placing TRAIP upstream of both. The NEIL3 and FA/BRCA pathways are non-epistatic: NEIL3 is the primary pathway and FA/BRCA is activated only when NEIL3 is absent.\",\n      \"method\": \"Co-immunoprecipitation (NEIL3–RUVBL1/2); siRNA knockdown epistasis analysis; laser-induced damage recruitment assays; DSB quantification (γH2AX); ICL sensitivity assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP for RUVBL1/2 interaction, genetic epistasis with multiple knockdowns, DSB measurement, multiple orthogonal methods\",\n      \"pmids\": [\"31980815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The tandem GRF-type zinc finger (Zf-GRF) domain of NEIL3 provides greater affinity and specificity for ssDNA than each individual motif alone. Crystal structure of the GRF domain shows a flexible head-to-tail configuration suited for binding multiple ssDNA conformations. Functionally, the NEIL3 GRF domain inhibits (autoinhibits) glycosylase activity against both monoadducts and ICLs, distinguishing it from other GRF-ZF domains that typically enhance catalytic activity.\",\n      \"method\": \"Crystal structure of GRF domain; ssDNA binding assays; glycosylase activity assays comparing full-length vs. truncated NEIL3; ICL unhooking assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus functional biochemical assays demonstrating autoinhibition, multiple substrates tested in one study\",\n      \"pmids\": [\"32878989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Crystal structure of the NEIL3 tandem GRF zinc-finger domain bound to DNA, combined with a structure of the NEI catalytic domain in complex with a DNA reaction intermediate, enabled construction of a model explaining how the NEI and GRF domains cooperate to recognize an ICL at a DNA replication X-structure. The GRF domain preferentially binds replication fork structures.\",\n      \"method\": \"X-ray crystallography (GRF–DNA complex; NEI domain–DNA intermediate complex); biochemical ssDNA binding assays; structural modeling of ICL recognition\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — two crystal structures with functional biochemical validation in a single study\",\n      \"pmids\": [\"36155818\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The glycosylase domain of murine NEIL3 (MmuNEIL3-GD) selectively unhooks dA-AP ICLs located at the duplex/single-strand junction of splayed duplexes modeling the leading template strand of a replication fork. NEIL3 preferentially acts on the AP residue on the leading template strand. The same strand preference applies to a 5,6-dihydrothymine monoadduct, showing it is a general feature of the glycosylase. Other BER enzymes (tested) do not unhook the dA-AP ICL.\",\n      \"method\": \"In vitro glycosylase/ICL unhooking assays on defined splayed-duplex fork substrates with site-specific dA-AP ICL or DHT monoadduct; comparison to other BER enzymes\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstituted in vitro with defined substrates, systematic comparison, replication-fork geometry specificity established\",\n      \"pmids\": [\"31923807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Human NEIL3 cleaves psoralen-induced ICLs in three-stranded and four-stranded DNA substrates, generating unhooked DNA fragments containing either an abasic site or a psoralen-thymine monoadduct, without generating single-strand breaks. This activity distinguishes NEIL3 from NEIL1/Nei, which nick the DNA during unhooking.\",\n      \"method\": \"In vitro glycosylase assays on defined three-stranded and four-stranded psoralen-crosslinked DNA substrates; product analysis by gel electrophoresis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with defined substrates and comparison to NEIL1/Nei paralogs\",\n      \"pmids\": [\"29234069\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NEIL3 promotes the HR step of FA/BRCA-pathway ICL repair (for MMC and cisplatin ICLs) through its GRF zinc finger motifs, which recruit NEIL3 to DSB sites and mediate interaction with the DSB resection machinery (CtIP, MRE11-RAD50-NBS1 complex, DNA2). NEIL3 depletion reduces chromatin recruitment of resection factors, decreases end resection, and compromises HR.\",\n      \"method\": \"Co-immunoprecipitation (NEIL3 with CtIP, MRN, DNA2); chromatin fractionation; HR reporter assay; end-resection assays (RPA/BrdU ssDNA); siRNA knockdown\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, HR reporter, resection assay, and epistasis with multiple knockdowns in one study\",\n      \"pmids\": [\"36351389\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human NEIL3 and its glycosylase domain (1-290) display AP lyase activity specific for ssDNA but not dsDNA. This activity is abolished by N-terminal deletion and by mutations at the zinc-finger motif. Expression of NEIL3 partially rescues an E. coli nth nei double mutant from hydrogen peroxide sensitivity.\",\n      \"method\": \"In vitro AP lyase assays on ssDNA/dsDNA; N-terminal deletion mutants; zinc-finger mutants; in vivo complementation of E. coli nth nei mutant\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical assays and in vivo complementation, single lab, no replication; note this study found no glycosylase activity on modified bases (negative for base excision on tested substrates)\",\n      \"pmids\": [\"19170771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Neil3 is the main DNA glycosylase responsible for incising hydantoin lesions in ssDNA in mouse tissues (demonstrated using total cell extracts from Neil3-/- mice). Loss of Neil3 impairs self-renewal of neural stem/progenitor cells (NSPCs) and reduces proliferation of mouse embryonic fibroblasts. Neil3-/- MEFs are sensitive to paraquat (oxidative stress) and cisplatin (ICL-inducing agent).\",\n      \"method\": \"Cell extracts from Neil3-/- mice in glycosylase activity assays; neurosphere culture (self-renewal assay); MEF proliferation assays; paraquat and cisplatin sensitivity assays\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — glycosylase activity in tissue extracts plus KO cell phenotyping with multiple readouts, single lab\",\n      \"pmids\": [\"23305905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Neil3 knockout mice show reduced numbers of proliferating neuronal progenitors in the striatum and reduced neurogenesis after hypoxia-ischemia. Neil3-deficient neural stem/progenitor cells have reduced capacity to augment neurogenesis and reduced repair of oxidative base lesions in ssDNA.\",\n      \"method\": \"Neil3-/- mouse model; hypoxia-ischemia model; cell counting of neural progenitors; in vitro neurosphere expansion; ssDNA BER activity assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined KO mouse model with cellular phenotype and DNA repair activity measurement, single lab\",\n      \"pmids\": [\"22065741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Neil3-/- mice display learning/memory deficits and reduced anxiety-like behavior. Neural stem/progenitor cells from aged Neil3-/- mice show impaired proliferative capacity and reduced DNA repair activity (hydantoin excision in ssDNA). Hippocampal neurons in Neil3-/- mice display synaptic irregularities.\",\n      \"method\": \"Behavioral tests (learning/memory); neurosphere proliferation assays; glycosylase activity assays; synaptic morphology by electron microscopy in Neil3-/- mice\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse phenotype with multiple orthogonal readouts including DNA repair activity, single lab\",\n      \"pmids\": [\"22959434\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Mouse NEIL3 protein localizes to the nucleus as demonstrated by immunofluorescence microscopy. Neil3 mRNA is selectively expressed in hematopoietic tissues (thymus, spleen, bone marrow) and is upregulated in splenocytes after mitogen stimulation in vitro.\",\n      \"method\": \"Immunofluorescence microscopy with anti-NEIL3 antibody on recombinant mouse NEIL3; Northern blot and RT-PCR for tissue expression; mitogen stimulation of splenocytes\",\n      \"journal\": \"Journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by immunofluorescence, expression regulation confirmed by stimulation, but localization not functionally linked in same experiment\",\n      \"pmids\": [\"16428305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"hNEIL3 expression is cell cycle regulated: it is repressed in quiescent cells (G0) and induced in early S phase upon mitogenic stimulation, under control of the Ras-dependent ERK-MAP kinase pathway. This regulation parallels that of the replication protein FEN1, suggesting a replication-associated repair function.\",\n      \"method\": \"Cell cycle synchronization; Western blot and qRT-PCR for hNEIL3 protein and mRNA levels; ERK pathway inhibitor experiments; comparison to hNEIL1 and hNEIL2 expression\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological pathway inhibition establishing ERK-MAP kinase regulation, multiple time points and methods, single lab\",\n      \"pmids\": [\"22365498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Human NEIL3 preferentially excises oxidized bases (5-hydroxyuracil, thymine glycol) from ssDNA and within open fork structures, while NEIL1 acts preferentially on dsDNA including damage upstream of the replication fork. Both enzymes act in concert at model replication fork substrates to remove oxidized bases from different structural contexts.\",\n      \"method\": \"In vitro glycosylase assays on model replication fork substrates with site-specific oxidized bases; comparison of NEIL1 and NEIL3 activity on ssDNA, dsDNA, and fork structures\",\n      \"journal\": \"Genes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro reconstitution with defined fork substrates, single lab, single study\",\n      \"pmids\": [\"31018584\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEIL3 co-localizes with TRF2 and repairs oxidative DNA lesions at telomeres specifically during mitosis. NEIL3-depleted HCC cells accumulate oxidative DNA lesions at telomeres, leading to telomere dysfunctional foci and 53BP1 foci. Upon oxidative DNA damage during mitosis, NEIL3 relocates to telomeres and recruits APE1, and NEIL3 (but not NEIL1 or NEIL2) is required to initiate APE1- and POLB-dependent BER at oxidized telomeres.\",\n      \"method\": \"META-FISH; immunofluorescence co-localization; NEIL3 knockdown (siRNA/shRNA) with telomere damage quantification; co-localization of NEIL3 and APE1 at telomeres; comparison to NEIL1 and NEIL2 knockdown\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional consequence, telomere-specific repair activity, comparison to paralogs, single lab\",\n      \"pmids\": [\"34045188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The NEIL3 Zf-GRF repeat (tandem, not single GRF motif) binds APE1 (but not APE2) via protein-protein interaction. This interaction suppresses APE1 endonuclease activity on ssDNA but not dsDNA, and excess NEIL3 Zf-GRF repeat reduces DNA damage in oxidative stress in Xenopus egg extracts.\",\n      \"method\": \"Protein-protein interaction assays (pull-down); APE1 endonuclease activity assays on ssDNA/dsDNA in presence of NEIL3 Zf-GRF; COMET assays in Xenopus egg extracts\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding assay plus functional APE1 inhibition assay plus cell-free system validation, single lab\",\n      \"pmids\": [\"32817342\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NEIL3 is required for PCNA- and FEN1-dependent long-patch BER at telomeres during S/G2 phase, and loss of NEIL3 causes anaphase DNA bridging due to telomere dysfunction; NEIL3 expression peaks in late S/G2 phase.\",\n      \"method\": \"Cell cycle synchronization and Western blot for NEIL3 levels; ChIP for telomere association; siRNA knockdown with anaphase bridge quantification; co-IP of NEIL3 with PCNA and FEN1\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ChIP, cell biology phenotype, cell cycle analysis, multiple methods, single lab\",\n      \"pmids\": [\"28854357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Mouse NEIL3 (MmuNEIL3Δ324) excises NM-Fapy-dG from ssDNA (but not dsDNA), while it cannot excise AFB1-Fapy-dG from either ssDNA or dsDNA. Product formation from ssDNA was incomplete and follows a single turnover rate of ~0.4 min-1.\",\n      \"method\": \"In vitro glycosylase assays on defined ssDNA and dsDNA oligonucleotides containing NM-Fapy-dG or AFB1-Fapy-dG; single turnover kinetics\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro reconstitution with defined substrates and kinetics, single lab, single study\",\n      \"pmids\": [\"30448017\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Loss of NEIL3 significantly increases spontaneous replication-associated DSBs and RPA recruitment, while decreasing Rad51 on nascent DNA at the replication fork, indicating that NEIL3 is required for HR-dependent repair at stalled forks. NEIL3 localizes to DSB sites during oxidative DNA damage and replication stress. NEIL3-deficient glioblastoma cells are sensitized to ATR inhibitor alone or combined with PARP1 inhibitor.\",\n      \"method\": \"NEIL3 knockdown (siRNA); γH2AX foci quantification; iPOND (isolation of proteins on nascent DNA) for Rad51 and RPA; ATR inhibitor sensitivity assays; immunofluorescence for NEIL3 at DSB sites\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — iPOND for replication-fork protein recruitment plus KO phenotype with multiple DNA damage readouts, single lab\",\n      \"pmids\": [\"29348879\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NEIL3 interacts with the 26S proteasome in a cisplatin-dependent manner (identified by proteomics) and mediates proteasomal degradation of WRNIP1, a protein involved in the early step of ICL repair. This facilitates a timely transition from lesion recognition to repair at ICL-stalled replication forks.\",\n      \"method\": \"Co-immunoprecipitation (NEIL3–26S proteasome); proteomic analysis; WRNIP1 degradation assay; gain- and loss-of-function experiments with cisplatin treatment\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and proteomic identification of 26S proteasome interaction, WRNIP1 degradation assay, single lab, single study\",\n      \"pmids\": [\"36997601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Loss of Neil3 in mice causes increased mortality after myocardial infarction due to myocardial rupture. Neil3-/- hearts show increased proliferation of fibroblasts and myofibroblasts post-MI. Genome-wide analysis reveals changes in 5mC and 5hmC in the cardiac epigenome, particularly in genes related to proliferation and myofibroblast differentiation, suggesting NEIL3-dependent modulation of DNA methylation regulates cardiac fibroblast behavior.\",\n      \"method\": \"Neil3-/- mouse MI model; survival analysis; histology; genome-wide 5mC/5hmC profiling; fibroblast proliferation quantification\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse model with defined phenotype, genome-wide epigenome analysis, multiple cellular readouts; mechanism (methylation regulation) inferred from correlation data\",\n      \"pmids\": [\"28052262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Neil3 deficiency in VSMCs promotes a shift towards a proliferating, lipid-accumulating, secretory macrophage-like phenotype (transdifferentiation) associated with increased Akt signaling pathway activity. NEIL3-abrogated human primary aortic VSMCs show Akt-dependent proliferation. These effects occur without changes in DNA damage levels, suggesting a non-canonical role for NEIL3 in VSMC phenotype regulation.\",\n      \"method\": \"Neil3-/- Apoe-/- mouse model; siRNA knockdown of NEIL3 in human primary aortic VSMCs; BrdU proliferation assay; Western blot for Akt phosphorylation; Akt inhibitor experiments; single-cell RNA sequencing and proteomics\",\n      \"journal\": \"Atherosclerosis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse model plus human cell knockdown with pathway inhibition, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"33714552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NEIL3 directly interacts with the EMT transcription factor TWIST1 and induces transcription of MDR1 (ABCB1) and BRAF genes through E-box promoter elements recognized by TWIST1, leading to BRAF/MEK/ERK pathway-mediated cell proliferation and drug resistance in HCC.\",\n      \"method\": \"Co-immunoprecipitation (NEIL3–TWIST1); RNA-seq; invasion/migration assays; mouse orthotopic HCC model; BRAF/MEK/ERK pathway analysis by Western blot; promoter reporter assays\",\n      \"journal\": \"The Journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct Co-IP of NEIL3–TWIST1, promoter reporter, in vivo mouse model, multiple readouts; single lab\",\n      \"pmids\": [\"36181299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"E2F1 transcriptionally activates NEIL3 expression, and NEIL3 overexpression in turn activates the cyclin D1-Rb-E2F1 pathway, forming a positive feedback loop that promotes cell proliferation and cell cycle progression in clear cell renal cell carcinoma.\",\n      \"method\": \"ChIP; luciferase reporter assay; siRNA/overexpression experiments; Western blot; cell proliferation and cell cycle assays; in vivo xenograft\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — ChIP and reporter assay establish transcriptional regulation, but mechanistic link between NEIL3 and cyclin D1-Rb-E2F1 relies on Western blot and overexpression without direct biochemical interaction evidence; single lab\",\n      \"pmids\": [\"37992567\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SNHG3 increases E2F1 binding to the NEIL3 promoter region, thereby activating NEIL3 transcription in hepatocellular carcinoma cells. NEIL3 participates in SNHG3-mediated regulation of HCC cell cycle, apoptosis, and proliferation (rescue experiments).\",\n      \"method\": \"ChIP assay (E2F1 binding to NEIL3 promoter); luciferase reporter; siRNA knockdown of SNHG3; rescue experiments with NEIL3 overexpression; CCK-8; flow cytometry\",\n      \"journal\": \"Immunogenetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — ChIP establishes E2F1–NEIL3 promoter binding, rescue experiments link NEIL3 to SNHG3 pathway, but molecular mechanism of NEIL3 in proliferation not defined; single lab\",\n      \"pmids\": [\"36114381\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NEIL3 deficiency leads to reduced PV+ GABAergic interneurons, impaired perineuronal net (PNN) integrity, altered hippocampal oscillatory dynamics (increased beta and low gamma power; reduced high gamma and ripple activity), and distinct effects on contextual vs. trace fear memory. Transcriptomic analysis reveals dysregulation of glutamatergic/GABAergic signaling genes, including Gabra2 downregulation potentially driven by changes in promoter DNA methylation.\",\n      \"method\": \"Neil3-/- mouse model; immunofluorescence (PV+ interneuron counting); PNN staining; in vivo electrophysiology (hippocampal oscillations); fear conditioning behavioral paradigms; RNA sequencing; bisulfite sequencing (DNA methylation)\",\n      \"journal\": \"Progress in neurobiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 2 / Weak — multiple readouts in KO model but mechanism linking NEIL3 DNA repair to PV+ interneuron regulation is not directly established biochemically; single lab, no replication\",\n      \"pmids\": [\"41015225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NEIL3 deficiency impairs adult hippocampal neurogenesis and behavioral pattern separation through altered transcriptional regulation of the Wnt signaling pathway, not through decreased genomic integrity. NEIL3-deficient adult-born neurons show reduced mature-like membrane properties.\",\n      \"method\": \"Neil3-/- mouse model; neurosphere proliferation and differentiation assays; behavioral pattern separation tests; electrophysiology of adult-born neurons; RNA sequencing; Wnt pathway inhibitor experiments\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 2 / Weak — KO model with multiple phenotypic readouts and pathway analysis, but direct molecular link between NEIL3 and Wnt pathway regulation not established biochemically; single lab\",\n      \"pmids\": [\"40035863\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NEIL3 is a DNA glycosylase of the Fpg/Nei superfamily that initiates base excision repair by excising oxidized purine and pyrimidine lesions (particularly hydantoins Sp and Gh, FapyG, FapyA, and thymine glycol) with a marked preference for single-stranded DNA and DNA fork structures, using its N-terminal valine as the catalytic nucleophile to form a Schiff base intermediate and acting primarily as a monofunctional glycosylase (β-elimination only); its C-terminal tandem GRF zinc-finger domain binds ssDNA with high affinity, autoinhibits glycosylase activity, and mediates interaction with APE1 to suppress aberrant ssDNA cleavage; during S phase NEIL3 is recruited via TRAIP-dependent CMG helicase ubiquitylation and through interaction with TRF1 to repair oxidative lesions at telomeres and to unhook replication fork-stalled interstrand cross-links (psoralen- and abasic site-derived) by direct N-glycosyl bond cleavage without generating double-strand breaks—the preferred ICL repair route that acts upstream of the FANCI-FANCD2/Fanconi anemia pathway; additionally, NEIL3 promotes the homologous recombination step of FA-pathway repair via GRF-mediated interaction with CtIP, MRN, and DNA2, and cooperates with RUVBL1/2 in psoralen-ICL repair; beyond canonical BER, NEIL3 interacts with TWIST1 to activate EMT gene programs and has non-canonical roles in regulating cardiac fibroblast proliferation, vascular smooth muscle cell phenotype (via Akt signaling), and adult hippocampal neurogenesis (partly through Wnt signaling).\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NEIL3 is a DNA glycosylase of the Fpg/Nei superfamily that initiates base excision repair of oxidized DNA lesions, with a marked preference for single-stranded DNA and replication-fork structures [#1, #18]. It excises oxidized purine hydantoins (spiroiminodihydantoin, guanidinohydantoin), FapyG, FapyA, and thymine glycol, but not 8-oxoG [#1, #2], and uniquely among mammalian glycosylases removes thymine glycol from quadruplex/telomeric DNA [#3]. Unlike its paralogs NEIL1/NEIL2, NEIL3 acts as a monofunctional glycosylase (β-elimination only) using its N-terminal valine rather than proline as the catalytic nucleophile to form a Schiff base intermediate; the V2P mutation converts it to a bifunctional enzyme and Lys81 is essential for catalysis [#1, #2]. Structural studies of the mouse glycosylase domain explain both its inability to excise 8-oxoG (loss of the αF-β9/10 capping loop) and its ssDNA preference (an unfavorable electrostatic environment for the opposite strand) [#4]. Its C-terminal tandem GRF zinc-finger domain binds ssDNA and replication-fork structures with high affinity, autoinhibits glycosylase activity, and mediates an interaction with APE1 that suppresses aberrant APE1 endonuclease cleavage of ssDNA [#7, #8, #20]. NEIL3 defines a replication-coupled, incision-independent pathway for unhooking interstrand cross-links: it cleaves one of the two N-glycosyl bonds of psoralen- and abasic-site-derived ICLs without generating double-strand breaks, acting upstream of and as the preferred route over the FANCI-FANCD2/Fanconi anemia pathway, which is engaged only when N-glycosyl cleavage fails [#0, #9, #10]. During S/G2 phase NEIL3 is recruited to telomeres through interaction with TRF1 and to ICLs through PARP- and TRAIP-dependent signaling, cooperating with RUVBL1/2, PCNA, and FEN1 to repair oxidative and cross-link damage and prevent telomere dysfunction and anaphase bridging [#5, #6, #19, #21]. Through its GRF domain NEIL3 also promotes the homologous-recombination step of FA/BRCA ICL repair by recruiting the resection machinery CtIP, MRN, and DNA2 [#11, #23]. Beyond DNA repair, NEIL3 interacts with the EMT factor TWIST1 to drive proliferation and drug-resistance gene programs in cancer, and its expression is cell-cycle regulated via the Ras-ERK pathway and transcriptionally controlled by E2F1 [#17, #27, #28]. Knockout mouse studies link NEIL3 to neural stem/progenitor self-renewal, hippocampal neurogenesis, and cardiac fibroblast regulation [#13, #14, #25].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Establishing NEIL3 as a bona fide glycosylase answered whether this Fpg/Nei member had catalytic activity and defined its unusual substrate range and chemistry.\",\n      \"evidence\": \"In vitro glycosylase assays, Schiff-base trapping, and E. coli triple-mutant complementation with mouse Neil3\",\n      \"pmids\": [\"20185759\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the structural basis for ssDNA preference\", \"Human enzyme catalytic mode not yet defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defining the catalytic mechanism and structure clarified why NEIL3 is monofunctional and ssDNA-selective and cannot process 8-oxoG.\",\n      \"evidence\": \"Active-site mutagenesis (V2P, K81) and a 2.0 Å crystal structure of the mouse glycosylase domain with substrate profiling including quadruplex DNA\",\n      \"pmids\": [\"23755964\", \"23313161\", \"23926102\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address how the C-terminal GRF domain regulates catalysis\", \"In-cell substrate spectrum not established\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"An early biochemical characterization established AP lyase activity specific for ssDNA and the requirement of the N-terminus and zinc-finger motif.\",\n      \"evidence\": \"In vitro AP lyase assays with deletion/zinc-finger mutants and E. coli complementation of human NEIL3\",\n      \"pmids\": [\"19170771\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No glycosylase activity on modified bases detected in this study\", \"Single lab, no replication\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Discovery of incision-independent ICL unhooking answered how cross-links can be repaired without double-strand breaks and placed NEIL3 upstream of the Fanconi anemia pathway.\",\n      \"evidence\": \"Xenopus egg-extract replication-coupled repair with genetic epistasis against FANCI-FANCD2 and biochemical unhooking assays\",\n      \"pmids\": [\"27693351\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Recruitment signal to the fork not yet defined\", \"Structural basis of ICL recognition unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identifying telomeric recruitment and BER partner interactions established a cell-cycle-coupled role at telomeres and connected NEIL3 to long-patch BER.\",\n      \"evidence\": \"Co-IP and co-localization with TRF1/TRF2, in vitro activity enhancement by TRF1, anaphase-bridge quantification in knockdown cells; psoralen-ICL cleavage in multi-stranded substrates\",\n      \"pmids\": [\"28854357\", \"29234069\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TRF1 enhances enzymatic activity mechanistically unknown\", \"Telomere vs. genome-wide division of labor not quantified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defining replication-fork geometry preference showed that NEIL3 acts on lesions on the leading template strand and shares fork substrates with NEIL1.\",\n      \"evidence\": \"In vitro unhooking and glycosylase assays on splayed-duplex and model fork substrates with site-specific dA-AP ICLs, DHT, and oxidized bases\",\n      \"pmids\": [\"31923807\", \"31018584\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Single-lab fork substrate models\", \"Coordination with NEIL1 in cells not demonstrated\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Characterizing the GRF domain and its partners answered how NEIL3 binds ssDNA, restrains its own activity, and controls APE1 during repair.\",\n      \"evidence\": \"Crystal structure of the tandem GRF domain, ssDNA-binding and autoinhibition assays, APE1/RUVBL1-2 pull-downs and activity assays, PARP/TRAIP epistasis in human cells\",\n      \"pmids\": [\"32878989\", \"32817342\", \"31980815\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How autoinhibition is relieved at the lesion is unclear\", \"TRAIP-to-NEIL3 recruitment signal not biochemically defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Structural modeling of GRF-DNA and catalytic-domain-intermediate complexes provided a coherent model for how the two domains cooperate to recognize an ICL at a replication X-structure.\",\n      \"evidence\": \"Two crystal structures (GRF-DNA; NEI domain-DNA intermediate) with biochemical ssDNA-binding validation\",\n      \"pmids\": [\"36155818\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length enzyme-fork complex not solved\", \"Dynamics of domain handoff not captured\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defining a GRF-dependent role in HR resection answered how NEIL3 also contributes to the Fanconi-anemia/BRCA branch of ICL repair when used for MMC and cisplatin lesions.\",\n      \"evidence\": \"Co-IP with CtIP/MRN/DNA2, chromatin fractionation, end-resection and HR reporter assays with knockdowns; complemented by iPOND-based fork data\",\n      \"pmids\": [\"36351389\", \"29348879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether resection role requires glycosylase activity is unresolved\", \"Direct vs. bridging interactions with resection factors not distinguished\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Telomere-specific oxidative repair during mitosis established NEIL3 as the dedicated initiator of APE1/POLB BER at oxidized telomeres, distinct from NEIL1/NEIL2.\",\n      \"evidence\": \"META-FISH, co-localization with TRF2 and APE1, telomere-damage quantification with paralog comparison in HCC cells\",\n      \"pmids\": [\"34045188\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single cancer-cell context\", \"Mechanism of mitosis-specific recruitment not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identifying proteasome-dependent WRNIP1 degradation suggested NEIL3 also coordinates the lesion-recognition-to-repair transition at ICL-stalled forks.\",\n      \"evidence\": \"Proteomics, Co-IP of NEIL3 with 26S proteasome, and WRNIP1 degradation assays under cisplatin\",\n      \"pmids\": [\"36997601\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether NEIL3 directly targets WRNIP1 to the proteasome unclear\", \"Single lab, single study\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linking NEIL3 to TWIST1 and to E2F1 transcriptional circuits revealed non-canonical, repair-independent roles in cancer proliferation and drug resistance.\",\n      \"evidence\": \"Co-IP of NEIL3-TWIST1, promoter reporters, RNA-seq and orthotopic models in HCC; ChIP/reporter for E2F1-NEIL3 feedback in renal carcinoma\",\n      \"pmids\": [\"36181299\", \"28052262\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the glycosylase activity is required for transcriptional functions unknown\", \"Direct vs. indirect TWIST1 cooperation not fully resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Cell-cycle and pathway regulation of NEIL3 expression connected it to replication-associated repair, paralleling FEN1.\",\n      \"evidence\": \"Cell-cycle synchronization, ERK-pathway inhibition, and qRT-PCR/Western analysis of human NEIL3\",\n      \"pmids\": [\"22365498\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct transcription factors at the promoter not all identified here\", \"Link to repair function correlative\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Knockout mouse phenotyping established physiological roles of NEIL3 in neural stem-cell self-renewal, neurogenesis, and behavior, and confirmed it as the principal ssDNA hydantoin glycosylase in tissue.\",\n      \"evidence\": \"Neil3-/- mice with neurosphere, MEF proliferation, behavioral, electron-microscopy, hypoxia-ischemia, and tissue-extract glycosylase assays\",\n      \"pmids\": [\"23305905\", \"22065741\", \"22959434\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether neural phenotypes require glycosylase activity not established\", \"Causal repair-to-phenotype link inferred\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Recent knockout studies attributed neural and behavioral phenotypes to transcriptional/epigenetic rather than genomic-integrity mechanisms, including Wnt-pathway and DNA-methylation effects.\",\n      \"evidence\": \"Neil3-/- mice with electrophysiology, fear conditioning, neurosphere assays, RNA-seq, bisulfite sequencing, and Wnt-inhibitor experiments\",\n      \"pmids\": [\"41015225\", \"40035863\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Direct biochemical link between NEIL3 and Wnt/methylation not established\", \"Single-lab models without independent replication\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Cardiovascular knockout studies indicated non-canonical roles for NEIL3 in cardiac fibroblast and vascular smooth muscle cell behavior, possibly via epigenetic and Akt signaling.\",\n      \"evidence\": \"Neil3-/- mouse MI and Apoe-/- models, human VSMC knockdown, 5mC/5hmC profiling, Akt phosphorylation and inhibitor assays, scRNA-seq\",\n      \"pmids\": [\"28052262\", \"33714552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting NEIL3 to DNA methylation and Akt is correlative\", \"Effects reported without changes in DNA damage levels\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NEIL3's canonical glycosylase chemistry relates mechanistically to its repair-independent transcriptional, epigenetic, and signaling roles remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No experiment separates catalytic-dependent from catalytic-independent functions in vivo\", \"No structure of the full-length enzyme engaging a replication fork\", \"No direct demonstration that NEIL3 enzymatically alters DNA methylation marks\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140097\", \"supporting_discovery_ids\": [0, 1, 2, 3, 9, 10, 18, 22]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [7, 8, 12, 20]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 9, 10, 12]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [27]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [16]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [5, 19, 21]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 6, 11, 23]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [5, 9, 18, 21]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [17, 21]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TRF1\", \"APE1\", \"PCNA\", \"FEN1\", \"RUVBL1\", \"CtIP\", \"DNA2\", \"TWIST1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":10,"faith_total":10,"faith_pct":100.0}}