{"gene":"ARL14EP","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2011,"finding":"ARL14EP (ARF7EP) functions as an effector protein of the GTPase ARL14/ARF7, forming a complex that recruits the motor protein myosin 1E; this ARL14–ARF7EP–myosin 1E complex drives movement of MHC-II vesicles along the actin cytoskeleton in human dendritic cells.","method":"Genome-wide RNAi screen followed by high-throughput flow cytometry assays for MHC-II expression and peptide loading; functional characterization in human dendritic cells","journal":"Cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — large-scale functional screen with follow-up mechanistic characterization in primary human DCs; single lab, pathway placement established but reconstitution/structural validation not described in abstract","pmids":["21458045"],"is_preprint":false},{"year":2018,"finding":"The C. elegans ortholog ARLE-14 (ARL14EP) binds to the histone H3K9 methyltransferase MET-2 (SETDB1 ortholog) and promotes its stable association with chromatin; together with LIN-65, this complex regulates the timing of heterochromatin domain formation during embryogenesis.","method":"Co-immunoprecipitation/binding assays identifying MET-2 complex components; genetic loss-of-function analysis with heterochromatin formation readouts in C. elegans embryos","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assays plus genetic epistasis in C. elegans, single lab, two orthogonal methods","pmids":["30140741"],"is_preprint":false},{"year":2019,"finding":"C11orf46 (ARL14EP) is a nuclear protein required for transcallosal axonal connectivity; knockdown causes dysconnectivity rescued by wild-type but not the C11orf46-R236H intellectual-disability mutant; C11orf46 represses axonal development genes (e.g., Sema6a) through association with the SETDB1 repressor complex, and locus-specific recruitment of C11orf46 via dCas9-SunTag normalizes SEMA6A expression and rescues connectivity via repressive chromatin remodeling.","method":"shRNA knockdown in neurons with in vivo transcallosal projection readout; rescue experiments with wild-type vs. R236H mutant C11orf46; RNA-guided epigenetic editing (dCas9-SunTag) targeting Sema6a promoter; chromatin remodeling assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with specific phenotypic readout, domain-mutant rescue, and functional epigenetic editing with mechanistic chromatin readout in two orthogonal experimental systems","pmids":["31511512"],"is_preprint":false},{"year":2023,"finding":"The crystal structure of human SETDB2 methyl-CpG-binding domain (MBD) in complex with the cysteine-rich domain of C11orf46 (ARL14EP) reveals that the non-canonical MBD has lost methylated-DNA-binding ability and instead uses its conserved basic concave surface, an arginine finger motif, a unique N-terminal extension, and intermolecular β-sheet formation to engage the cysteine-rich domain of C11orf46 as a protein–protein interaction surface.","method":"X-ray crystallography of SETDB2 MBD–C11orf46 complex; structure-based analysis of interaction interface","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structure with detailed interface characterization, independently noted in a companion commentary (PMID:38458157)","pmids":["38159574","38458157"],"is_preprint":false},{"year":2024,"finding":"In C. elegans, ARLE-14 (ARL14EP ortholog) works with MET-2/SETDB1 and LIN-65/ATF7IP to antagonize SET-25-driven random monoallelic silencing; MET-2's catalytic SET domain is required, and ARLE-14 promotes MET-2 chromatin association, placing ARL14EP in a pathway that prevents somatic monoallelic expression during embryonic development.","method":"Genetic epistasis analysis using loss-of-function mutants in C. elegans; monoallelic expression reporters in whole tissues; catalytic SET-domain mutants","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with catalytic domain mutants and reporter assays; single lab, replicated in preprint and peer-reviewed publication","pmids":["41315265","38328214"],"is_preprint":false}],"current_model":"ARL14EP (C11orf46/ARF7EP) is a multifunctional effector/adaptor protein that: (1) in immune cells binds ARL14/ARF7 and recruits myosin 1E to drive actin-based MHC-II vesicle transport; (2) in neurons localizes to the nucleus where it associates with the SETDB1 repressor complex to repress axonal guidance genes (e.g., Sema6a) and thereby supports transcallosal connectivity; and (3) structurally, its cysteine-rich domain docks onto the non-canonical MBD of SETDB1/SETDB2, replacing DNA binding with a protein–protein interaction surface that stabilizes the methyltransferase at chromatin—a mechanism conserved from C. elegans (ARLE-14/MET-2) to humans."},"narrative":{"mechanistic_narrative":"ARL14EP (ARF7EP/C11orf46) is a bifunctional adaptor protein that operates both in cytoplasmic vesicle transport and in chromatin-based transcriptional repression [PMID:21458045, PMID:31511512]. In human dendritic cells it acts as an effector of the GTPase ARL14/ARF7, bridging the activated GTPase to the motor protein myosin 1E to drive actin-based movement of MHC-II vesicles [PMID:21458045]. In neurons it is a nuclear protein that associates with the SETDB1 repressor complex to silence axonal guidance genes such as Sema6a, an activity required for transcallosal axonal connectivity; an intellectual-disability-associated R236H mutant fails to rescue this connectivity, and locus-specific recruitment via dCas9-SunTag normalizes SEMA6A expression through repressive chromatin remodeling [PMID:31511512]. Its conserved cysteine-rich domain mediates this chromatin role by docking onto the non-canonical methyl-CpG-binding domain of SETDB2, which has lost methylated-DNA binding and instead presents a basic concave surface, an arginine finger, and an intermolecular β-sheet as a protein–protein interaction interface that stabilizes the methyltransferase at chromatin [PMID:38159574, PMID:38458157]. This methyltransferase-stabilizing function is conserved to the C. elegans ortholog ARLE-14, which promotes chromatin association of MET-2/SETDB1 together with LIN-65/ATF7IP to regulate the timing of heterochromatin formation and to antagonize SET-25-driven monoallelic silencing during embryogenesis [PMID:30140741, PMID:41315265, PMID:38328214].","teleology":[{"year":2011,"claim":"Established the first molecular function of ARL14EP, defining it as a GTPase effector that physically links ARL14/ARF7 to a myosin motor for cytoskeletal cargo transport.","evidence":"Genome-wide RNAi screen with flow-cytometry MHC-II readouts and complex characterization in primary human dendritic cells","pmids":["21458045"],"confidence":"Medium","gaps":["No reconstitution or structural validation of the ARL14–ARF7EP–myosin 1E complex","Whether this vesicle-transport role operates outside dendritic cells is untested","Connection between this cytoplasmic role and the later nuclear/chromatin role is unresolved"]},{"year":2018,"claim":"Identified a distinct chromatin-associated role by showing the C. elegans ortholog binds the H3K9 methyltransferase MET-2/SETDB1 and stabilizes it on chromatin to time heterochromatin formation.","evidence":"Co-immunoprecipitation/binding assays and genetic loss-of-function with heterochromatin readouts in C. elegans embryos","pmids":["30140741"],"confidence":"Medium","gaps":["Mechanism by which binding promotes chromatin stabilization not defined at this stage","Conservation to the human protein not yet demonstrated","Single-lab finding using two methods"]},{"year":2019,"claim":"Demonstrated the human nuclear function and disease relevance: ARL14EP represses axonal guidance genes via the SETDB1 repressor complex to support brain connectivity, with a point mutation abolishing this role.","evidence":"shRNA knockdown with in vivo transcallosal projection readouts, wild-type vs R236H rescue, and dCas9-SunTag epigenetic editing of the Sema6a promoter in neurons","pmids":["31511512"],"confidence":"High","gaps":["Full set of target genes beyond Sema6a not catalogued","How nuclear localization is regulated relative to the cytoplasmic effector role is unknown","Direct contribution of R236H to interface disruption not structurally resolved here"]},{"year":2023,"claim":"Provided the structural basis for chromatin recruitment, showing the ARL14EP cysteine-rich domain engages a non-canonical SETDB2 MBD that has repurposed its DNA-binding surface for protein–protein interaction.","evidence":"X-ray crystallography of the SETDB2 MBD–C11orf46 cysteine-rich domain complex with interface analysis","pmids":["38159574","38458157"],"confidence":"High","gaps":["Structure of the complex with full-length SETDB1 not determined","Functional impact of the R236H mutation on the resolved interface not tested in the structure","How interface engagement translates into methyltransferase stabilization in vivo not shown"]},{"year":2024,"claim":"Refined the chromatin pathway by placing ARL14EP/ARLE-14 in a MET-2/LIN-65 module that antagonizes SET-25-driven monoallelic silencing, requiring catalytic methyltransferase activity.","evidence":"Genetic epistasis with catalytic SET-domain mutants and monoallelic expression reporters in C. elegans","pmids":["41315265","38328214"],"confidence":"Medium","gaps":["Whether the monoallelic-silencing antagonism is conserved in mammals is untested","Single-lab finding","Direct biochemical link between ARLE-14 binding and SET domain catalysis not established"]},{"year":null,"claim":"How a single protein partitions between a cytoplasmic GTPase-effector/vesicle-transport role and a nuclear methyltransferase-stabilizing role, and whether these functions are coordinated, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No study connects the ARL14/myosin 1E vesicle function with the SETDB1 chromatin function","Regulation of subcellular partitioning is uncharacterized","Mammalian role in monoallelic expression untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,3]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,4]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0]}],"complexes":["SETDB1 repressor complex","ARL14–ARF7EP–myosin 1E complex"],"partners":["ARL14","MYO1E","SETDB1","SETDB2","MET-2","LIN-65","ATF7IP"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N8R7","full_name":"ARL14 effector protein","aliases":["ARF7 effector protein"],"length_aa":260,"mass_kda":29.3,"function":"Through its interaction with ARL14 and MYO1E, may connect MHC class II-containing cytoplasmic vesicles to the actin network and hence controls the movement of these vesicles along the actin cytoskeleton in dendritic cells","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q8N8R7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ARL14EP","classification":"Not Classified","n_dependent_lines":6,"n_total_lines":1208,"dependency_fraction":0.004966887417218543},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000152219","cell_line_id":"CID000499","localizations":[{"compartment":"nuclear_punctae","grade":3},{"compartment":"chromatin","grade":2},{"compartment":"membrane","grade":2},{"compartment":"nucleoplasm","grade":2}],"interactors":[{"gene":"ATF7IP","stoichiometry":10.0},{"gene":"SETDB1","stoichiometry":10.0},{"gene":"SNAP29","stoichiometry":10.0},{"gene":"ARPC1A","stoichiometry":4.0},{"gene":"ATF7IP2","stoichiometry":0.2},{"gene":"BCOR","stoichiometry":0.2},{"gene":"RPS27A;UBC;UBB;UBA52","stoichiometry":0.2},{"gene":"YWHAZ","stoichiometry":0.2},{"gene":"YWHAH","stoichiometry":0.2},{"gene":"YWHAG","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000499","total_profiled":1310},"omim":[{"mim_id":"612295","title":"ADP-RIBOSYLATION FACTOR-LIKE GTPase 14 EFFECTOR PROTEIN; ARL14EP","url":"https://www.omim.org/entry/612295"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"},{"location":"Focal adhesion sites","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Nucleoli","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ARL14EP"},"hgnc":{"alias_symbol":["FLJ38968","ARF7EP"],"prev_symbol":["C11orf46"]},"alphafold":{"accession":"Q8N8R7","domains":[{"cath_id":"-","chopping":"5-67","consensus_level":"high","plddt":93.679,"start":5,"end":67},{"cath_id":"-","chopping":"72-134","consensus_level":"medium","plddt":87.3775,"start":72,"end":134},{"cath_id":"-","chopping":"190-260","consensus_level":"medium","plddt":87.5582,"start":190,"end":260}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N8R7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N8R7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N8R7-F1-predicted_aligned_error_v6.png","plddt_mean":80.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ARL14EP","jax_strain_url":"https://www.jax.org/strain/search?query=ARL14EP"},"sequence":{"accession":"Q8N8R7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N8R7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N8R7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N8R7"}},"corpus_meta":[{"pmid":"21458045","id":"PMC_21458045","title":"A Genome-wide multidimensional RNAi screen reveals pathways controlling MHC class II antigen presentation.","date":"2011","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/21458045","citation_count":120,"is_preprint":false},{"pmid":"30140741","id":"PMC_30140741","title":"Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos.","date":"2018","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/30140741","citation_count":56,"is_preprint":false},{"pmid":"31511512","id":"PMC_31511512","title":"In vivo epigenetic editing of Sema6a promoter reverses transcallosal dysconnectivity caused by C11orf46/Arl14ep risk gene.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31511512","citation_count":48,"is_preprint":false},{"pmid":"35413103","id":"PMC_35413103","title":"Candidate genes for polycystic ovary syndrome are regulated by TGFβ in the bovine foetal ovary.","date":"2022","source":"Human reproduction (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/35413103","citation_count":21,"is_preprint":false},{"pmid":"32678441","id":"PMC_32678441","title":"Analysis of expression of candidate genes for polycystic ovary syndrome in adult and fetal human and fetal bovine ovaries†.","date":"2020","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/32678441","citation_count":18,"is_preprint":false},{"pmid":"36519390","id":"PMC_36519390","title":"Genome-wide gene by environment study of time spent in daylight and chronotype identifies emerging genetic architecture underlying light sensitivity.","date":"2023","source":"Sleep","url":"https://pubmed.ncbi.nlm.nih.gov/36519390","citation_count":17,"is_preprint":false},{"pmid":"33940579","id":"PMC_33940579","title":"CRISPR/dCas9 as a Therapeutic Approach for Neurodevelopmental Disorders: Innovations and Limitations Compared to Traditional Strategies.","date":"2021","source":"Developmental neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/33940579","citation_count":14,"is_preprint":false},{"pmid":"36720993","id":"PMC_36720993","title":"Transcriptome-wide association analyses identify an association between ARL14EP and polycystic ovary syndrome.","date":"2023","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36720993","citation_count":9,"is_preprint":false},{"pmid":"37223019","id":"PMC_37223019","title":"Genes in loci genetically associated with polycystic ovary syndrome are dynamically expressed in human fetal gonadal, metabolic and brain tissues.","date":"2023","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/37223019","citation_count":7,"is_preprint":false},{"pmid":"36011342","id":"PMC_36011342","title":"Unusual Presentation in WAGR Syndrome: Expanding the Phenotypic and Genotypic Spectrum of the Diseases.","date":"2022","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/36011342","citation_count":6,"is_preprint":false},{"pmid":"38159574","id":"PMC_38159574","title":"Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46.","date":"2023","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/38159574","citation_count":5,"is_preprint":false},{"pmid":"39299614","id":"PMC_39299614","title":"Bivariate genome-wide association study of circulating fibrinogen and C-reactive protein levels.","date":"2024","source":"Journal of thrombosis and haemostasis : JTH","url":"https://pubmed.ncbi.nlm.nih.gov/39299614","citation_count":3,"is_preprint":false},{"pmid":"38328214","id":"PMC_38328214","title":"Maternal histone methyltransferases antagonistically regulate monoallelic expression in C. elegans.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38328214","citation_count":2,"is_preprint":false},{"pmid":"38458157","id":"PMC_38458157","title":"One form and two functions: MBD of SETDB2 is a protein-interacting domain.","date":"2024","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/38458157","citation_count":1,"is_preprint":false},{"pmid":"41315265","id":"PMC_41315265","title":"Maternal histone methyltransferases antagonistically regulate autosomal random monoallelic expression (aRMAE) in C. elegans.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41315265","citation_count":0,"is_preprint":false},{"pmid":"41578317","id":"PMC_41578317","title":"Deciphering the shared genetic architecture between female reproductive disorders and psychiatric disorders.","date":"2026","source":"Journal of ovarian research","url":"https://pubmed.ncbi.nlm.nih.gov/41578317","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10622,"output_tokens":1574,"usd":0.027738,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8313,"output_tokens":2544,"usd":0.052582,"stage2_stop_reason":"end_turn"},"total_usd":0.08032,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"ARL14EP (ARF7EP) functions as an effector protein of the GTPase ARL14/ARF7, forming a complex that recruits the motor protein myosin 1E; this ARL14–ARF7EP–myosin 1E complex drives movement of MHC-II vesicles along the actin cytoskeleton in human dendritic cells.\",\n      \"method\": \"Genome-wide RNAi screen followed by high-throughput flow cytometry assays for MHC-II expression and peptide loading; functional characterization in human dendritic cells\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — large-scale functional screen with follow-up mechanistic characterization in primary human DCs; single lab, pathway placement established but reconstitution/structural validation not described in abstract\",\n      \"pmids\": [\"21458045\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The C. elegans ortholog ARLE-14 (ARL14EP) binds to the histone H3K9 methyltransferase MET-2 (SETDB1 ortholog) and promotes its stable association with chromatin; together with LIN-65, this complex regulates the timing of heterochromatin domain formation during embryogenesis.\",\n      \"method\": \"Co-immunoprecipitation/binding assays identifying MET-2 complex components; genetic loss-of-function analysis with heterochromatin formation readouts in C. elegans embryos\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assays plus genetic epistasis in C. elegans, single lab, two orthogonal methods\",\n      \"pmids\": [\"30140741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"C11orf46 (ARL14EP) is a nuclear protein required for transcallosal axonal connectivity; knockdown causes dysconnectivity rescued by wild-type but not the C11orf46-R236H intellectual-disability mutant; C11orf46 represses axonal development genes (e.g., Sema6a) through association with the SETDB1 repressor complex, and locus-specific recruitment of C11orf46 via dCas9-SunTag normalizes SEMA6A expression and rescues connectivity via repressive chromatin remodeling.\",\n      \"method\": \"shRNA knockdown in neurons with in vivo transcallosal projection readout; rescue experiments with wild-type vs. R236H mutant C11orf46; RNA-guided epigenetic editing (dCas9-SunTag) targeting Sema6a promoter; chromatin remodeling assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with specific phenotypic readout, domain-mutant rescue, and functional epigenetic editing with mechanistic chromatin readout in two orthogonal experimental systems\",\n      \"pmids\": [\"31511512\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The crystal structure of human SETDB2 methyl-CpG-binding domain (MBD) in complex with the cysteine-rich domain of C11orf46 (ARL14EP) reveals that the non-canonical MBD has lost methylated-DNA-binding ability and instead uses its conserved basic concave surface, an arginine finger motif, a unique N-terminal extension, and intermolecular β-sheet formation to engage the cysteine-rich domain of C11orf46 as a protein–protein interaction surface.\",\n      \"method\": \"X-ray crystallography of SETDB2 MBD–C11orf46 complex; structure-based analysis of interaction interface\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structure with detailed interface characterization, independently noted in a companion commentary (PMID:38458157)\",\n      \"pmids\": [\"38159574\", \"38458157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In C. elegans, ARLE-14 (ARL14EP ortholog) works with MET-2/SETDB1 and LIN-65/ATF7IP to antagonize SET-25-driven random monoallelic silencing; MET-2's catalytic SET domain is required, and ARLE-14 promotes MET-2 chromatin association, placing ARL14EP in a pathway that prevents somatic monoallelic expression during embryonic development.\",\n      \"method\": \"Genetic epistasis analysis using loss-of-function mutants in C. elegans; monoallelic expression reporters in whole tissues; catalytic SET-domain mutants\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with catalytic domain mutants and reporter assays; single lab, replicated in preprint and peer-reviewed publication\",\n      \"pmids\": [\"41315265\", \"38328214\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ARL14EP (C11orf46/ARF7EP) is a multifunctional effector/adaptor protein that: (1) in immune cells binds ARL14/ARF7 and recruits myosin 1E to drive actin-based MHC-II vesicle transport; (2) in neurons localizes to the nucleus where it associates with the SETDB1 repressor complex to repress axonal guidance genes (e.g., Sema6a) and thereby supports transcallosal connectivity; and (3) structurally, its cysteine-rich domain docks onto the non-canonical MBD of SETDB1/SETDB2, replacing DNA binding with a protein–protein interaction surface that stabilizes the methyltransferase at chromatin—a mechanism conserved from C. elegans (ARLE-14/MET-2) to humans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ARL14EP (ARF7EP/C11orf46) is a bifunctional adaptor protein that operates both in cytoplasmic vesicle transport and in chromatin-based transcriptional repression [#0, #2]. In human dendritic cells it acts as an effector of the GTPase ARL14/ARF7, bridging the activated GTPase to the motor protein myosin 1E to drive actin-based movement of MHC-II vesicles [#0]. In neurons it is a nuclear protein that associates with the SETDB1 repressor complex to silence axonal guidance genes such as Sema6a, an activity required for transcallosal axonal connectivity; an intellectual-disability-associated R236H mutant fails to rescue this connectivity, and locus-specific recruitment via dCas9-SunTag normalizes SEMA6A expression through repressive chromatin remodeling [#2]. Its conserved cysteine-rich domain mediates this chromatin role by docking onto the non-canonical methyl-CpG-binding domain of SETDB2, which has lost methylated-DNA binding and instead presents a basic concave surface, an arginine finger, and an intermolecular β-sheet as a protein–protein interaction interface that stabilizes the methyltransferase at chromatin [#3]. This methyltransferase-stabilizing function is conserved to the C. elegans ortholog ARLE-14, which promotes chromatin association of MET-2/SETDB1 together with LIN-65/ATF7IP to regulate the timing of heterochromatin formation and to antagonize SET-25-driven monoallelic silencing during embryogenesis [#1, #4].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established the first molecular function of ARL14EP, defining it as a GTPase effector that physically links ARL14/ARF7 to a myosin motor for cytoskeletal cargo transport.\",\n      \"evidence\": \"Genome-wide RNAi screen with flow-cytometry MHC-II readouts and complex characterization in primary human dendritic cells\",\n      \"pmids\": [\"21458045\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No reconstitution or structural validation of the ARL14–ARF7EP–myosin 1E complex\",\n        \"Whether this vesicle-transport role operates outside dendritic cells is untested\",\n        \"Connection between this cytoplasmic role and the later nuclear/chromatin role is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified a distinct chromatin-associated role by showing the C. elegans ortholog binds the H3K9 methyltransferase MET-2/SETDB1 and stabilizes it on chromatin to time heterochromatin formation.\",\n      \"evidence\": \"Co-immunoprecipitation/binding assays and genetic loss-of-function with heterochromatin readouts in C. elegans embryos\",\n      \"pmids\": [\"30140741\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which binding promotes chromatin stabilization not defined at this stage\",\n        \"Conservation to the human protein not yet demonstrated\",\n        \"Single-lab finding using two methods\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrated the human nuclear function and disease relevance: ARL14EP represses axonal guidance genes via the SETDB1 repressor complex to support brain connectivity, with a point mutation abolishing this role.\",\n      \"evidence\": \"shRNA knockdown with in vivo transcallosal projection readouts, wild-type vs R236H rescue, and dCas9-SunTag epigenetic editing of the Sema6a promoter in neurons\",\n      \"pmids\": [\"31511512\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Full set of target genes beyond Sema6a not catalogued\",\n        \"How nuclear localization is regulated relative to the cytoplasmic effector role is unknown\",\n        \"Direct contribution of R236H to interface disruption not structurally resolved here\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided the structural basis for chromatin recruitment, showing the ARL14EP cysteine-rich domain engages a non-canonical SETDB2 MBD that has repurposed its DNA-binding surface for protein–protein interaction.\",\n      \"evidence\": \"X-ray crystallography of the SETDB2 MBD–C11orf46 cysteine-rich domain complex with interface analysis\",\n      \"pmids\": [\"38159574\", \"38458157\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structure of the complex with full-length SETDB1 not determined\",\n        \"Functional impact of the R236H mutation on the resolved interface not tested in the structure\",\n        \"How interface engagement translates into methyltransferase stabilization in vivo not shown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Refined the chromatin pathway by placing ARL14EP/ARLE-14 in a MET-2/LIN-65 module that antagonizes SET-25-driven monoallelic silencing, requiring catalytic methyltransferase activity.\",\n      \"evidence\": \"Genetic epistasis with catalytic SET-domain mutants and monoallelic expression reporters in C. elegans\",\n      \"pmids\": [\"41315265\", \"38328214\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the monoallelic-silencing antagonism is conserved in mammals is untested\",\n        \"Single-lab finding\",\n        \"Direct biochemical link between ARLE-14 binding and SET domain catalysis not established\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single protein partitions between a cytoplasmic GTPase-effector/vesicle-transport role and a nuclear methyltransferase-stabilizing role, and whether these functions are coordinated, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No study connects the ARL14/myosin 1E vesicle function with the SETDB1 chromatin function\",\n        \"Regulation of subcellular partitioning is uncharacterized\",\n        \"Mammalian role in monoallelic expression untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"SETDB1 repressor complex\", \"ARL14–ARF7EP–myosin 1E complex\"],\n    \"partners\": [\"ARL14\", \"MYO1E\", \"SETDB1\", \"SETDB2\", \"MET-2\", \"LIN-65\", \"ATF7IP\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}