{"gene":"NIF3L1","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2003,"finding":"Mouse Nif3l1 interacts with Trip15/CSN2 (a transcriptional corepressor/COP9 signalosome component), confirmed by yeast two-hybrid, pull-down assay, and co-immunoprecipitation. Nif3l1 normally localizes to the cytoplasm but translocates to the nucleus during retinoic acid-primed neural differentiation of P19 cells, a translocation enhanced by enforced Trip15/CSN2 expression. Overexpression of sense Nif3l1 RNA enhanced neural differentiation with down-regulation of Oct-3/4 and induction of Mash-1. Luciferase reporter assays showed Nif3l1 acts as a transcriptional repressor and synergizes Trip15/CSN2-mediated repression.","method":"Yeast two-hybrid screening, pull-down assay, co-immunoprecipitation, overexpression/antisense inhibition in P19 cells, luciferase reporter assay, RT-PCR for marker genes","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Y2H, pull-down, Co-IP, reporter assay, loss-of-function via antisense) in a single focused study","pmids":["12522100"],"is_preprint":false},{"year":2003,"finding":"Human NIF3L1 interacts with itself (homodimerizes) and with a novel binding partner, NIF3L1 BP1 (a 23.67 kDa protein with a putative leucine zipper domain), as demonstrated by yeast two-hybrid and mammalian two-hybrid systems. Deletion analysis showed a C-terminal 100 amino acid region of NIF3L1 BP1 is sufficient for the interaction with NIF3L1. Co-transfection experiments revealed that NIF3L1 and NIF3L1 BP1 interact in the cytoplasm of human LNCaP cells.","method":"Yeast two-hybrid screen of HeLa cDNA library, mammalian two-hybrid confirmation, deletion analysis, co-transfection/co-localization in LNCaP cells","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple methods (Y2H, mammalian two-hybrid, deletion mapping, co-transfection) but no functional rescue or biochemical activity assay","pmids":["12951069"],"is_preprint":false},{"year":2004,"finding":"NIF3L1 was identified as a component of a single polypeptide complex in mammalian cells that includes WBSCR14 and four 14-3-3 isotypes, identified by co-immunoprecipitation. This places NIF3L1 as a binding partner of a glucose-responsive bHLH-LZ transcription factor complex.","method":"Co-immunoprecipitation (pull-down/complex identification in mammalian cells), interaction identified in context of WBSCR14 interactome screen","journal":"Human molecular genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — NIF3L1 is one of five interactors identified; no functional follow-up specific to NIF3L1 reported in abstract","pmids":["15163635"],"is_preprint":false},{"year":2000,"finding":"A GFP-NIF3L1 fusion protein localizes to the cytoplasm in transfected cells, establishing the baseline subcellular localization of the human NIF3L1 protein.","method":"GFP fusion protein expression and fluorescence microscopy","journal":"Cytogenetics and cell genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single method (GFP localization), no functional consequence tested","pmids":["11124544"],"is_preprint":false}],"current_model":"NIF3L1 is a highly conserved cytoplasmic protein that translocates to the nucleus during retinoic acid-induced neural differentiation, where it functions as a transcriptional repressor by physically interacting with and synergizing the corepressor Trip15/CSN2; it also homodimerizes, binds a novel leucine-zipper partner (NIF3L1 BP1) in the cytoplasm, and associates with the WBSCR14/14-3-3 transcription factor complex."},"narrative":{"mechanistic_narrative":"NIF3L1 is a conserved cytoplasmic protein that participates in transcriptional repression coupled to neural differentiation [PMID:12522100]. During retinoic acid-primed neural differentiation of P19 cells, NIF3L1 translocates from the cytoplasm to the nucleus, where it physically associates with the transcriptional corepressor Trip15/CSN2 (a COP9 signalosome component) and synergizes its repressive activity; enforced Trip15/CSN2 expression enhances this nuclear translocation [PMID:12522100]. Functionally, elevated NIF3L1 promotes neural differentiation with down-regulation of Oct-3/4 and induction of Mash-1, and reporter assays establish NIF3L1 itself as a transcriptional repressor [PMID:12522100]. NIF3L1 homodimerizes and binds a novel cytoplasmic leucine-zipper partner, NIF3L1 BP1, through a C-terminal region of the partner [PMID:12951069]. Beyond these interactions and its differentiation-associated repressor role, no catalytic activity or detailed mechanism of repression has been characterized in the available corpus.","teleology":[{"year":2000,"claim":"Establishing where the protein resides was the first step toward any functional model; NIF3L1 was shown to be cytoplasmic at baseline.","evidence":"GFP-NIF3L1 fusion expression and fluorescence microscopy in transfected cells","pmids":["11124544"],"confidence":"Low","gaps":["Single localization method with no functional consequence tested","Does not address regulated relocalization or stimulus-dependent trafficking"]},{"year":2003,"claim":"The central question of what NIF3L1 does was addressed by linking it to transcriptional repression and neural differentiation, showing it interacts with corepressor Trip15/CSN2 and translocates to the nucleus during differentiation.","evidence":"Yeast two-hybrid, pull-down, Co-IP, overexpression/antisense in P19 cells, luciferase reporter assays, and RT-PCR for differentiation markers","pmids":["12522100"],"confidence":"High","gaps":["The direct DNA-binding target genes of the NIF3L1/Trip15 repression are not defined","The molecular signal triggering cytoplasm-to-nucleus translocation is unresolved","No biochemical activity intrinsic to NIF3L1 identified"]},{"year":2003,"claim":"To map the protein's interaction surfaces, human NIF3L1 was shown to self-associate and to bind a novel cytoplasmic leucine-zipper partner (NIF3L1 BP1), extending its interactome beyond the nuclear repression machinery.","evidence":"Yeast and mammalian two-hybrid systems, deletion mapping, and co-transfection/co-localization in LNCaP cells","pmids":["12951069"],"confidence":"Medium","gaps":["Functional role of the NIF3L1/NIF3L1 BP1 interaction is untested","No rescue or activity assay tying the homodimer/partner binding to repression or differentiation"]},{"year":2004,"claim":"An interactome screen placed NIF3L1 within a WBSCR14/14-3-3 transcription factor complex, hinting at a broader transcriptional/metabolic regulatory context.","evidence":"Co-immunoprecipitation complex identification in mammalian cells within a WBSCR14 interactome screen","pmids":["15163635"],"confidence":"Low","gaps":["NIF3L1 is one of five interactors with no NIF3L1-specific functional follow-up","Direct versus indirect association within the complex not resolved"]},{"year":null,"claim":"The biochemical activity of NIF3L1 and the identity of the genes it represses remain undefined.","evidence":"No catalytic assay or genome-wide target mapping reported in the timeline","pmids":[],"confidence":"Low","gaps":["No enzymatic or structural mechanism for repression established","Direct DNA-binding targets unknown","Trigger for nuclear translocation uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[0]}],"complexes":[],"partners":["TRIP15/CSN2","NIF3L1","NIF3L1 BP1","WBSCR14"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9GZT8","full_name":"NIF3-like protein 1","aliases":["Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 1 protein"],"length_aa":377,"mass_kda":42.0,"function":"May function as a transcriptional corepressor through its interaction with COPS2, negatively regulating the expression of genes involved in neuronal differentiation","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9GZT8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NIF3L1","classification":"Not Classified","n_dependent_lines":10,"n_total_lines":1208,"dependency_fraction":0.008278145695364239},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NIF3L1","total_profiled":1310},"omim":[{"mim_id":"611965","title":"THO COMPLEX, SUBUNIT 7; THOC7","url":"https://www.omim.org/entry/611965"},{"mim_id":"605778","title":"NIF3-LIKE 1; NIF3L1","url":"https://www.omim.org/entry/605778"},{"mim_id":"605678","title":"MLX-INTERACTING PROTEIN-LIKE; MLXIPL","url":"https://www.omim.org/entry/605678"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NIF3L1"},"hgnc":{"alias_symbol":["CALS-7","MDS015"],"prev_symbol":["ALS2CR1"]},"alphafold":{"accession":"Q9GZT8","domains":[{"cath_id":"3.40.1390.30","chopping":"27-126_345-365","consensus_level":"high","plddt":97.5096,"start":27,"end":365},{"cath_id":"3.40.1390.30","chopping":"133-156_246-337","consensus_level":"high","plddt":97.9337,"start":133,"end":337},{"cath_id":"3.30.70.260","chopping":"166-238","consensus_level":"high","plddt":89.9015,"start":166,"end":238}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZT8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZT8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZT8-F1-predicted_aligned_error_v6.png","plddt_mean":91.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NIF3L1","jax_strain_url":"https://www.jax.org/strain/search?query=NIF3L1"},"sequence":{"accession":"Q9GZT8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9GZT8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9GZT8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZT8"}},"corpus_meta":[{"pmid":"15163635","id":"PMC_15163635","title":"The subcellular localization of the ChoRE-binding protein, encoded by the Williams-Beuren syndrome critical region gene 14, is regulated by 14-3-3.","date":"2004","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/15163635","citation_count":62,"is_preprint":false},{"pmid":"11161814","id":"PMC_11161814","title":"Cloning and characterization of three novel genes, ALS2CR1, ALS2CR2, and ALS2CR3, in the juvenile amyotrophic lateral sclerosis (ALS2) critical region at chromosome 2q33-q34: candidate genes for ALS2.","date":"2001","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/11161814","citation_count":41,"is_preprint":false},{"pmid":"12522100","id":"PMC_12522100","title":"The role of transcriptional corepressor Nif3l1 in early stage of neural differentiation via cooperation with Trip15/CSN2.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12522100","citation_count":27,"is_preprint":false},{"pmid":"12951069","id":"PMC_12951069","title":"Identification and characterization of NIF3L1 BP1, a novel cytoplasmic interaction partner of the NIF3L1 protein.","date":"2003","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/12951069","citation_count":17,"is_preprint":false},{"pmid":"11124544","id":"PMC_11124544","title":"Isolation and characterization of a novel human gene, NIF3L1, and its mouse ortholog, Nif3l1, highly conserved from bacteria to mammals.","date":"2000","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11124544","citation_count":15,"is_preprint":false},{"pmid":"31934183","id":"PMC_31934183","title":"Relationship between osteoporosis and osteoarthritis based on DNA methylation.","date":"2019","source":"International journal of clinical and experimental pathology","url":"https://pubmed.ncbi.nlm.nih.gov/31934183","citation_count":12,"is_preprint":false},{"pmid":"37371576","id":"PMC_37371576","title":"The Ubiquitin-Proteasome System Participates in Sperm Surface Subproteome Remodeling during Boar Sperm Capacitation.","date":"2023","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/37371576","citation_count":11,"is_preprint":false},{"pmid":"38585359","id":"PMC_38585359","title":"Serum biomarkers in patients with drug-resistant epilepsy: a proteomics-based analysis.","date":"2024","source":"Frontiers in neurology","url":"https://pubmed.ncbi.nlm.nih.gov/38585359","citation_count":6,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6211,"output_tokens":1224,"usd":0.018496,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7787,"output_tokens":1816,"usd":0.042167,"stage2_stop_reason":"end_turn"},"total_usd":0.060663,"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\": 2003,\n      \"finding\": \"Mouse Nif3l1 interacts with Trip15/CSN2 (a transcriptional corepressor/COP9 signalosome component), confirmed by yeast two-hybrid, pull-down assay, and co-immunoprecipitation. Nif3l1 normally localizes to the cytoplasm but translocates to the nucleus during retinoic acid-primed neural differentiation of P19 cells, a translocation enhanced by enforced Trip15/CSN2 expression. Overexpression of sense Nif3l1 RNA enhanced neural differentiation with down-regulation of Oct-3/4 and induction of Mash-1. Luciferase reporter assays showed Nif3l1 acts as a transcriptional repressor and synergizes Trip15/CSN2-mediated repression.\",\n      \"method\": \"Yeast two-hybrid screening, pull-down assay, co-immunoprecipitation, overexpression/antisense inhibition in P19 cells, luciferase reporter assay, RT-PCR for marker genes\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Y2H, pull-down, Co-IP, reporter assay, loss-of-function via antisense) in a single focused study\",\n      \"pmids\": [\"12522100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Human NIF3L1 interacts with itself (homodimerizes) and with a novel binding partner, NIF3L1 BP1 (a 23.67 kDa protein with a putative leucine zipper domain), as demonstrated by yeast two-hybrid and mammalian two-hybrid systems. Deletion analysis showed a C-terminal 100 amino acid region of NIF3L1 BP1 is sufficient for the interaction with NIF3L1. Co-transfection experiments revealed that NIF3L1 and NIF3L1 BP1 interact in the cytoplasm of human LNCaP cells.\",\n      \"method\": \"Yeast two-hybrid screen of HeLa cDNA library, mammalian two-hybrid confirmation, deletion analysis, co-transfection/co-localization in LNCaP cells\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple methods (Y2H, mammalian two-hybrid, deletion mapping, co-transfection) but no functional rescue or biochemical activity assay\",\n      \"pmids\": [\"12951069\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"NIF3L1 was identified as a component of a single polypeptide complex in mammalian cells that includes WBSCR14 and four 14-3-3 isotypes, identified by co-immunoprecipitation. This places NIF3L1 as a binding partner of a glucose-responsive bHLH-LZ transcription factor complex.\",\n      \"method\": \"Co-immunoprecipitation (pull-down/complex identification in mammalian cells), interaction identified in context of WBSCR14 interactome screen\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — NIF3L1 is one of five interactors identified; no functional follow-up specific to NIF3L1 reported in abstract\",\n      \"pmids\": [\"15163635\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"A GFP-NIF3L1 fusion protein localizes to the cytoplasm in transfected cells, establishing the baseline subcellular localization of the human NIF3L1 protein.\",\n      \"method\": \"GFP fusion protein expression and fluorescence microscopy\",\n      \"journal\": \"Cytogenetics and cell genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single method (GFP localization), no functional consequence tested\",\n      \"pmids\": [\"11124544\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NIF3L1 is a highly conserved cytoplasmic protein that translocates to the nucleus during retinoic acid-induced neural differentiation, where it functions as a transcriptional repressor by physically interacting with and synergizing the corepressor Trip15/CSN2; it also homodimerizes, binds a novel leucine-zipper partner (NIF3L1 BP1) in the cytoplasm, and associates with the WBSCR14/14-3-3 transcription factor complex.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NIF3L1 is a conserved cytoplasmic protein that participates in transcriptional repression coupled to neural differentiation [#0]. During retinoic acid-primed neural differentiation of P19 cells, NIF3L1 translocates from the cytoplasm to the nucleus, where it physically associates with the transcriptional corepressor Trip15/CSN2 (a COP9 signalosome component) and synergizes its repressive activity; enforced Trip15/CSN2 expression enhances this nuclear translocation [#0]. Functionally, elevated NIF3L1 promotes neural differentiation with down-regulation of Oct-3/4 and induction of Mash-1, and reporter assays establish NIF3L1 itself as a transcriptional repressor [#0]. NIF3L1 homodimerizes and binds a novel cytoplasmic leucine-zipper partner, NIF3L1 BP1, through a C-terminal region of the partner [#1]. Beyond these interactions and its differentiation-associated repressor role, no catalytic activity or detailed mechanism of repression has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Establishing where the protein resides was the first step toward any functional model; NIF3L1 was shown to be cytoplasmic at baseline.\",\n      \"evidence\": \"GFP-NIF3L1 fusion expression and fluorescence microscopy in transfected cells\",\n      \"pmids\": [\"11124544\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single localization method with no functional consequence tested\", \"Does not address regulated relocalization or stimulus-dependent trafficking\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"The central question of what NIF3L1 does was addressed by linking it to transcriptional repression and neural differentiation, showing it interacts with corepressor Trip15/CSN2 and translocates to the nucleus during differentiation.\",\n      \"evidence\": \"Yeast two-hybrid, pull-down, Co-IP, overexpression/antisense in P19 cells, luciferase reporter assays, and RT-PCR for differentiation markers\",\n      \"pmids\": [\"12522100\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The direct DNA-binding target genes of the NIF3L1/Trip15 repression are not defined\", \"The molecular signal triggering cytoplasm-to-nucleus translocation is unresolved\", \"No biochemical activity intrinsic to NIF3L1 identified\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"To map the protein's interaction surfaces, human NIF3L1 was shown to self-associate and to bind a novel cytoplasmic leucine-zipper partner (NIF3L1 BP1), extending its interactome beyond the nuclear repression machinery.\",\n      \"evidence\": \"Yeast and mammalian two-hybrid systems, deletion mapping, and co-transfection/co-localization in LNCaP cells\",\n      \"pmids\": [\"12951069\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role of the NIF3L1/NIF3L1 BP1 interaction is untested\", \"No rescue or activity assay tying the homodimer/partner binding to repression or differentiation\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"An interactome screen placed NIF3L1 within a WBSCR14/14-3-3 transcription factor complex, hinting at a broader transcriptional/metabolic regulatory context.\",\n      \"evidence\": \"Co-immunoprecipitation complex identification in mammalian cells within a WBSCR14 interactome screen\",\n      \"pmids\": [\"15163635\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"NIF3L1 is one of five interactors with no NIF3L1-specific functional follow-up\", \"Direct versus indirect association within the complex not resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical activity of NIF3L1 and the identity of the genes it represses remain undefined.\",\n      \"evidence\": \"No catalytic assay or genome-wide target mapping reported in the timeline\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No enzymatic or structural mechanism for repression established\", \"Direct DNA-binding targets unknown\", \"Trigger for nuclear translocation uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TRIP15/CSN2\", \"NIF3L1\", \"NIF3L1 BP1\", \"WBSCR14\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}