{"gene":"RFX2","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":1992,"finding":"RFX2 was identified as a structurally similar protein to RFX1 with identical DNA binding features, involved in control of MHC class II gene expression, and mapped to chromosome 19p13.2-p13.3 by in situ hybridization.","method":"In situ hybridization, genomic mapping","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 — direct chromosomal localization, but functional characterization limited to structural similarity inference","pmids":["1505960"],"is_preprint":false},{"year":2004,"finding":"RFX2 was purified from rat testis nuclear extracts using the H1t TE1 X-box element as an affinity chromatography probe, identified as an 85 kDa protein that binds the X-box consensus element in the testis-specific histone H1t promoter, and co-expression of RFX2 activates the H1t promoter in germinal cell lines. Mutation of either TE1 or TE2 subelements represses activity.","method":"Affinity chromatography, EMSA with supershift, co-expression/reporter assay, mutagenesis","journal":"Journal of cellular biochemistry","confidence":"High","confidence_rationale":"Tier 1-2 — purification, EMSA, supershift, reporter assay with mutagenesis, multiple orthogonal methods in single study","pmids":["14743396"],"is_preprint":false},{"year":2004,"finding":"RFX2 forms a homodimer that binds the H1t-60 CCTAGG palindrome motif (X-box) in the testis-specific histone H1t promoter, and is highly expressed in pachytene spermatocytes and early round spermatids. RFX2 also binds X-box motifs in the lamin C2 and Sgy promoters.","method":"Competitive band-shift assay, immunoprecipitation with specific antisera, Western blot, immunohistochemistry, in vitro synthesis","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (EMSA, supershift, IHC, in vitro synthesis) establishing homodimer binding and target promoters","pmids":["15229132"],"is_preprint":false},{"year":2005,"finding":"RFX2 activates the H1t promoter by binding to either X-box element independently for partial activation, but simultaneous binding to both X-box elements (TE1 and TE2) is required for maximal promoter activation.","method":"Affinity chromatography, transient expression/reporter assay, site-directed mutagenesis","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 — reporter assay with double mutagenesis establishes cooperativity requirement","pmids":["15526285"],"is_preprint":false},{"year":2006,"finding":"RFX2 is the most abundant RFX family member in rat testis, enriched in spermatocyte nuclei where H1t transcription is upregulated; RFX2 levels decrease and RFX1 levels increase in early spermatids where H1t is downregulated, supporting a stage-specific regulatory switch.","method":"Western blot, EMSA with antibody supershift, subcellular fractionation across germ cell stages","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 — multiple cell-stage comparisons with EMSA, but functional consequence inferred rather than directly tested","pmids":["16676351"],"is_preprint":false},{"year":2008,"finding":"RFX2 binds the H1t X-box in vivo in spermatocytes (ChIP), and cooperates with NF-Y, which binds the adjacent CCAAT-box; NF-Y interacts directly or indirectly with RFX2, and both elements are required for promoter activity.","method":"ChIP, EMSA, Western blot, co-expression reporter assay, real-time RT-PCR","journal":"Journal of cellular biochemistry","confidence":"High","confidence_rationale":"Tier 1-2 — in vivo ChIP confirms binding, plus protein-protein interaction (NF-Y/RFX2) and functional mutagenesis of both elements","pmids":["18247329"],"is_preprint":false},{"year":2009,"finding":"A-MYB transcription factor binds MYB binding sites (MBS) in the Rfx2 promoter, occupies the promoter in vivo (ChIP), and is required for Rfx2 expression; Rfx2 expression is virtually eliminated in A-myb knockout testes. RFX2 in turn binds X-boxes in promoters of target genes Adam5, Pdcl2, Spag6, and Alf, and activates the Alf promoter in transfected cells (ChIP and co-transfection confirmed).","method":"Electrophoretic gel-shift, ChIP, co-transfection assay, A-myb knockout analysis, immunohistology","journal":"BMC developmental biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (EMSA, ChIP, co-transfection, KO) establishing upstream regulation by A-MYB and downstream targets of RFX2","pmids":["20003220"],"is_preprint":false},{"year":2011,"finding":"Rfx2 is expressed in ciliated tissues in Xenopus (neural tube, gastrocoel roof plate, epidermal multi-ciliated cells, otic vesicles, kidneys) and morpholino knockdown results in fewer or truncated cilia and loss of expression of ciliogenic target genes including TTC25; TTC25 is required for ciliogenesis, HH signaling, and left-right patterning.","method":"Morpholino knockdown, in situ hybridization, cilia imaging, epistasis","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 — loss-of-function with specific ciliary phenotype, target gene regulation, and epistasis established in vivo","pmids":["22227339"],"is_preprint":false},{"year":2011,"finding":"Rfx2 is expressed in motile cilia cells in mouse and zebrafish; morpholino knockdown of Rfx2 in zebrafish Kupffer's Vesicle reduces KV cilia length and causes left-right patterning defects including randomization of Nodal pathway genes (southpaw, lefty1, lefty2) and reversal of heart/gut primordia. Rfx2 is also required for ciliogenesis in zebrafish pronephric duct.","method":"Morpholino knockdown, in situ hybridization, cilia length measurement, LR patterning analysis, organ-specific transgenic rescue","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 — tissue-specific KD with defined molecular (Nodal pathway) and cellular (cilia length) phenotypes, plus transgenic rescue","pmids":["22233545"],"is_preprint":false},{"year":2014,"finding":"Rfx2 genomic occupancy (ChIP-seq) in Xenopus multi-ciliated cells identifies direct target genes controlling ciliogenesis, cilia function, and cell movement; Rfx2 cell-autonomously controls apical surface expansion in nascent multi-ciliated cells as revealed by in vivo cell biological imaging after Rfx2 depletion.","method":"ChIP-seq, RNA-seq, morpholino knockdown, in vivo live imaging, bioinformatics","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1-2 — genomic ChIP-seq plus in vivo live imaging with loss-of-function, multiple orthogonal approaches","pmids":["24424412"],"is_preprint":false},{"year":2015,"finding":"Rfx2 knockout in mice causes complete male sterility with arrest of spermatid development prior to elongation; arrested spermatids show altered Golgi organization, failure to form an acrosomal cap from proacrosomal vesicles, and complete failure to form the flagellar axoneme. ChIP-seq and RNA-seq identified 139 direct RFX2 target genes during spermiogenesis, enriched in ciliary function genes.","method":"Targeted gene knockout, RNA-seq, ChIP-seq, histology, electron microscopy","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 1-2 — knockout with defined ultrastructural phenotypes, genome-wide direct target identification by ChIP-seq/RNA-seq","pmids":["26162102"],"is_preprint":false},{"year":2015,"finding":"Rfx2 gene trap null mice are viable without neural tube or situs defects but Rfx2gt/gt males are infertile due to spermatid maturation defects at or before round/elongating spermatid stage; lacZ reporter shows Rfx2 expression in ciliated tissues including node, floor plate, and dorsal neural tube.","method":"Gene trap knockout, lacZ reporter, RT-PCR, fertility testing, histology","journal":"Genesis","confidence":"Medium","confidence_rationale":"Tier 2 — clean null allele with confirmed mRNA loss, defined spermatogenic phenotype","pmids":["26248850"],"is_preprint":false},{"year":2016,"finding":"Rfx2 knockout in mice causes arrest of spermatogenesis at an early round spermatid step; round spermatids detach from seminiferous tubules forming multinucleated giant cells that undergo apoptosis; flagellum formation is inhibited at its earliest stage. RNA-seq and ChIP-PCR identified numerous direct RFX2 target genes including cilia-related and testis-specific genes.","method":"Knockout mouse, RNA-seq, ChIP-PCR, histology, TUNEL assay","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 — independent replication of knockout phenotype from separate lab, with direct target confirmation by ChIP","pmids":["26853561"],"is_preprint":false},{"year":2023,"finding":"RFX2 binds to the PAF1 promoter (ChIP-qPCR) and activates PAF1 transcription (dual-luciferase assay) in spinal ependymoma cells, thereby promoting tumor stemness; PAF1 overexpression rescues the effects of RFX2 knockdown on stem cell features and malignant progression.","method":"ChIP-qPCR, dual-luciferase reporter assay, RFX2 knockdown, in vivo xenograft","journal":"Journal of neuro-oncology","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct promoter binding confirmed by ChIP and luciferase, with rescue experiment, but single lab","pmids":["38057505"],"is_preprint":false},{"year":2025,"finding":"ACK1 kinase interacts with RFX2 through its MHR domain (co-immunoprecipitation, mass spectrometry) and competitively inhibits RFX2 ubiquitination by E3 ligase MIB1; ACK1 inhibition promotes MIB1-mediated RFX2 ubiquitination and degradation, thereby relieving RFX2 transcriptional suppression of BNIP3 (confirmed by luciferase reporter and ChIP), leading to mitophagy activation.","method":"Co-IP, mass spectrometry, ChIP, luciferase reporter assay, ubiquitination assay","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (MS, Co-IP, ChIP, reporter, ubiquitination assay) in single study establishing mechanism","pmids":["40715489"],"is_preprint":false},{"year":2025,"finding":"RFX2 binds the RASSF1 promoter (ChIP) and activates RASSF1 transcription (dual-luciferase assay); loss of RFX2 in lung adenocarcinoma downregulates RASSF1, reducing YAP phosphorylation and impairing Hippo signaling, thereby promoting immune escape from CD8+ T cells.","method":"ChIP, dual-luciferase reporter assay, RFX2 overexpression, co-culture with CD8+ T cells, in vivo tumor model","journal":"Cell division","confidence":"Medium","confidence_rationale":"Tier 2-3 — direct promoter binding confirmed by ChIP and luciferase, pathway placement via Hippo signaling, single lab","pmids":["40069841"],"is_preprint":false},{"year":2025,"finding":"SWI/SNF complex component Actl6a maintains expression of rfx2 (and foxj1a) in zebrafish pronephros; depletion of Actl6a reduces chromatin accessibility and SWI/SNF binding at rfx2 locus; overexpression of rfx2 mRNA partially rescues cystic kidney and cilia disassembly in actl6a mutants, placing rfx2 downstream of SWI/SNF in the epigenetic control of ciliogenesis.","method":"ATAC-seq, ChIP, morpholino/CRISPR knockout, mRNA rescue, omics analyses in zebrafish","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — multiple omics methods plus genetic rescue, but preprint and single lab","pmids":["bio_10.1101_2025.06.10.658863"],"is_preprint":true}],"current_model":"RFX2 is a winged-helix transcription factor that binds X-box DNA elements as a homodimer to directly activate target gene transcription; it is itself transcriptionally activated by A-MYB in spermatocytes and regulated post-translationally by ACK1-dependent protection from MIB1-mediated ubiquitination; in multi-ciliated cells RFX2 serves as a master coordinator of ciliogenesis (controlling axoneme assembly, cilia function genes) and apical cell morphogenesis, while in spermatids it governs acrosome formation and flagellar axoneme biogenesis through direct regulation of ~139 target genes, and in cancer contexts it suppresses BNIP3 transcription and activates RASSF1/Hippo signaling."},"narrative":{"teleology":[{"year":1992,"claim":"Identification of RFX2 as a second RFX family member with conserved DNA-binding features established that X-box recognition is mediated by a multi-gene family, not a single factor.","evidence":"Genomic mapping and in situ hybridization to chromosome 19p13","pmids":["1505960"],"confidence":"Medium","gaps":["No functional assay performed; role inferred from structural similarity to RFX1","No target gene regulation demonstrated"]},{"year":2004,"claim":"Biochemical purification and functional assays resolved that RFX2 is the X-box-binding transcription factor in spermatocytes, forming homodimers on the H1t promoter and activating transcription in germinal cells.","evidence":"Affinity chromatography from rat testis extracts, EMSA with supershift, reporter assays with mutagenesis, competitive band-shift, immunohistochemistry","pmids":["14743396","15229132"],"confidence":"High","gaps":["Homodimerization not structurally resolved","No in vivo occupancy data yet"]},{"year":2005,"claim":"Demonstrating that both X-box elements in the H1t promoter must be simultaneously occupied for full activation established a cooperative binding mechanism for RFX2.","evidence":"Reporter assays with single and double X-box mutations","pmids":["15526285"],"confidence":"Medium","gaps":["Cooperativity mechanism (protein-protein contact vs. chromatin looping) not defined","Single reporter system"]},{"year":2008,"claim":"In vivo ChIP confirmation of RFX2 at the H1t promoter, combined with discovery of NF-Y as a cooperating partner at the adjacent CCAAT-box, revealed a combinatorial transcription logic for spermatocyte-specific gene expression.","evidence":"ChIP in spermatocytes, EMSA, co-expression reporter assays","pmids":["18247329"],"confidence":"High","gaps":["Direct physical interaction between RFX2 and NF-Y not confirmed by reciprocal Co-IP or structural data","Whether this cooperativity applies genome-wide is unknown"]},{"year":2009,"claim":"Placing RFX2 downstream of A-MYB and identifying additional spermatogenic target genes (Adam5, Pdcl2, Spag6, Alf) established RFX2 as a central node in a transcriptional hierarchy governing spermiogenesis.","evidence":"ChIP on Rfx2 and target promoters, A-myb knockout testes showing loss of Rfx2 expression, co-transfection reporter assays","pmids":["20003220"],"confidence":"High","gaps":["Whether A-MYB regulation of Rfx2 is direct in all species not confirmed","Genome-wide target identification not yet performed"]},{"year":2011,"claim":"Loss-of-function studies in Xenopus and zebrafish established RFX2 as a master regulator of motile ciliogenesis, required for cilia length, left-right patterning, and expression of ciliogenic target genes like TTC25.","evidence":"Morpholino knockdown in Xenopus epidermis and zebrafish Kupffer's vesicle/pronephric duct, cilia imaging, Nodal pathway gene expression analysis, transgenic rescue","pmids":["22227339","22233545"],"confidence":"High","gaps":["Genetic knockout not yet performed in these organisms","Whether RFX2 acts cell-autonomously in all ciliated tissues not resolved"]},{"year":2014,"claim":"Genome-wide ChIP-seq in Xenopus multi-ciliated cells defined the direct RFX2 regulon and revealed a previously unknown cell-autonomous role in apical surface expansion during multi-ciliated cell differentiation.","evidence":"ChIP-seq, RNA-seq, morpholino knockdown, in vivo live imaging in Xenopus","pmids":["24424412"],"confidence":"High","gaps":["Mechanism linking RFX2 transcriptional targets to apical surface remodeling not defined","Overlap with RFX3 targets not fully delineated"]},{"year":2015,"claim":"Mouse knockouts from two independent groups demonstrated that RFX2 is dispensable for viability and left-right patterning but absolutely required for spermiogenesis, governing acrosome biogenesis and flagellar axoneme assembly through ~139 direct target genes.","evidence":"Targeted knockout and gene-trap null mice, ChIP-seq, RNA-seq, electron microscopy, histology, fertility testing","pmids":["26162102","26248850"],"confidence":"High","gaps":["Redundancy with RFX3/RFX4 in ciliated somatic tissues not formally tested","How RFX2 controls Golgi-to-acrosome vesicle trafficking is mechanistically unclear"]},{"year":2016,"claim":"An independent knockout confirmed spermatid arrest and added the observation that RFX2-null spermatids detach from the seminiferous epithelium and undergo apoptosis as multinucleated giant cells, establishing the severity of the maturation block.","evidence":"Knockout mouse, RNA-seq, ChIP-PCR, TUNEL assay","pmids":["26853561"],"confidence":"High","gaps":["Whether detachment is a direct consequence of RFX2 target loss or secondary to differentiation failure not resolved"]},{"year":2025,"claim":"Discovery that ACK1 physically protects RFX2 from MIB1-mediated ubiquitination and degradation established the first post-translational regulatory mechanism for RFX2 protein stability, linking kinase signaling to transcriptional output.","evidence":"Co-IP, mass spectrometry, ubiquitination assays, ChIP, luciferase reporter in cancer cell lines","pmids":["40715489"],"confidence":"High","gaps":["Whether ACK1 phosphorylates RFX2 or acts solely by competitive binding not determined","Relevance of ACK1–MIB1 axis to normal spermatogenesis or ciliogenesis not tested"]},{"year":2025,"claim":"Identification of RASSF1 as a direct RFX2 target in lung adenocarcinoma connected RFX2 transcriptional activity to Hippo pathway regulation and anti-tumor immunity.","evidence":"ChIP, dual-luciferase reporter, RFX2 overexpression, co-culture with CD8+ T cells, in vivo tumor model","pmids":["40069841"],"confidence":"Medium","gaps":["Single-lab finding; independent replication needed","Whether RFX2–RASSF1 axis operates in normal tissues unknown","Mechanism of RFX2 downregulation in tumors not established"]},{"year":null,"claim":"Key open questions include how RFX2 functionally partitions from RFX3/RFX4 at shared ciliary targets, the structural basis of RFX2 homodimerization and X-box cooperativity, the in vivo relevance of ACK1/MIB1-mediated RFX2 turnover outside cancer cells, and the mechanism by which RFX2 target genes drive acrosome vesicle trafficking.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of RFX2 dimer–DNA complex exists","Redundancy with other RFX paralogs in somatic cilia not genetically dissected","Post-translational regulation in physiological (non-cancer) contexts unexplored"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,2,5,6,9,10]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,3,5,6,9,10,13,14,15]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2,4,5]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[7,8,9,10]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[10,11,12]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[7,8]}],"complexes":[],"partners":["NF-Y","ACK1","MIB1","A-MYB"],"other_free_text":[]},"mechanistic_narrative":"RFX2 is a winged-helix transcription factor that binds X-box DNA motifs as a homodimer to activate transcription of genes governing ciliogenesis, spermiogenesis, and cell identity. RFX2 directly occupies X-box elements in promoters of cilia-related and testis-specific genes, and its cooperative binding to tandem X-box sites—together with cofactors such as NF-Y—is required for maximal promoter activation [PMID:15229132, PMID:18247329, PMID:14743396]. In multi-ciliated cells, RFX2 orchestrates axoneme assembly, cilia function gene expression, and apical surface remodeling, while in spermatids it is essential for acrosome formation and flagellar axoneme biogenesis; Rfx2 knockout mice are viable but exhibit complete male sterility due to spermatid arrest prior to elongation [PMID:24424412, PMID:26162102, PMID:22227339]. RFX2 protein stability is regulated post-translationally by ACK1, which shields RFX2 from MIB1-mediated ubiquitination and proteasomal degradation, linking RFX2 turnover to downstream transcriptional outputs including BNIP3 repression and mitophagy control [PMID:40715489]."},"prefetch_data":{"uniprot":{"accession":"P48378","full_name":"DNA-binding protein RFX2","aliases":["Regulatory factor X 2"],"length_aa":723,"mass_kda":80.0,"function":"Transcription factor that acts as a key regulator of spermatogenesis. Acts by regulating expression of genes required for the haploid phase during spermiogenesis, such as genes required for cilium assembly and function (By similarity). Recognizes and binds the X-box, a regulatory motif with DNA sequence 5'-GTNRCC(0-3N)RGYAAC-3' present on promoters (PubMed:10330134). Probably activates transcription of the testis-specific histone gene H1-6 (By similarity)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P48378/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RFX2","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RFX2","total_profiled":1310},"omim":[{"mim_id":"620506","title":"INTRAFLAGELLAR TRANSPORT 46; IFT46","url":"https://www.omim.org/entry/620506"},{"mim_id":"619466","title":"CILIARY DYSKINESIA, PRIMARY, 47, AND LISSENCEPHALY; CILD47","url":"https://www.omim.org/entry/619466"},{"mim_id":"612659","title":"REGULATORY FACTOR X, 6; RFX6","url":"https://www.omim.org/entry/612659"},{"mim_id":"601990","title":"TUMOR PROTEIN p73; TP73","url":"https://www.omim.org/entry/601990"},{"mim_id":"601863","title":"REGULATORY FACTOR X, 5; RFX5","url":"https://www.omim.org/entry/601863"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Basal body","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"testis","ntpm":55.3}],"url":"https://www.proteinatlas.org/search/RFX2"},"hgnc":{"alias_symbol":["FLJ14226"],"prev_symbol":[]},"alphafold":{"accession":"P48378","domains":[{"cath_id":"1.10.10.10","chopping":"173-277","consensus_level":"high","plddt":82.0887,"start":173,"end":277},{"cath_id":"-","chopping":"344-404_424-518","consensus_level":"medium","plddt":91.3919,"start":344,"end":518},{"cath_id":"1.10.490","chopping":"531-682","consensus_level":"high","plddt":89.4309,"start":531,"end":682}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P48378","model_url":"https://alphafold.ebi.ac.uk/files/AF-P48378-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P48378-F1-predicted_aligned_error_v6.png","plddt_mean":67.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RFX2","jax_strain_url":"https://www.jax.org/strain/search?query=RFX2"},"sequence":{"accession":"P48378","fasta_url":"https://rest.uniprot.org/uniprotkb/P48378.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P48378/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P48378"}},"corpus_meta":[{"pmid":"24424412","id":"PMC_24424412","title":"Coordinated 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reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/36922987","citation_count":2,"is_preprint":false},{"pmid":"40715489","id":"PMC_40715489","title":"RFX2-BNIP3 axis-driven adaptive mitophagy promotes resistance to ACK1-targeted therapy in non-small cell lung cancer.","date":"2025","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/40715489","citation_count":1,"is_preprint":false},{"pmid":"40069841","id":"PMC_40069841","title":"RFX2 downregulates RASSF1 expression and YAP phosphorylation through Hippo signaling to promote immune escape in lung adenocarcinoma.","date":"2025","source":"Cell division","url":"https://pubmed.ncbi.nlm.nih.gov/40069841","citation_count":1,"is_preprint":false},{"pmid":"35145545","id":"PMC_35145545","title":"The First Report of a Missense Variant in RFX2 Causing Non-Syndromic Tooth Agenesis in a Consanguineous Pakistani Family.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35145545","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.10.658863","title":"Epigenetic regulation of cilia stability and kidney by the chromatin remodeling SWI/SNF complexes","date":"2025-06-14","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.10.658863","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12749,"output_tokens":4101,"usd":0.049881},"stage2":{"model":"claude-opus-4-6","input_tokens":7534,"output_tokens":2812,"usd":0.161955},"total_usd":0.211836,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1992,\n      \"finding\": \"RFX2 was identified as a structurally similar protein to RFX1 with identical DNA binding features, involved in control of MHC class II gene expression, and mapped to chromosome 19p13.2-p13.3 by in situ hybridization.\",\n      \"method\": \"In situ hybridization, genomic mapping\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct chromosomal localization, but functional characterization limited to structural similarity inference\",\n      \"pmids\": [\"1505960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RFX2 was purified from rat testis nuclear extracts using the H1t TE1 X-box element as an affinity chromatography probe, identified as an 85 kDa protein that binds the X-box consensus element in the testis-specific histone H1t promoter, and co-expression of RFX2 activates the H1t promoter in germinal cell lines. Mutation of either TE1 or TE2 subelements represses activity.\",\n      \"method\": \"Affinity chromatography, EMSA with supershift, co-expression/reporter assay, mutagenesis\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — purification, EMSA, supershift, reporter assay with mutagenesis, multiple orthogonal methods in single study\",\n      \"pmids\": [\"14743396\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RFX2 forms a homodimer that binds the H1t-60 CCTAGG palindrome motif (X-box) in the testis-specific histone H1t promoter, and is highly expressed in pachytene spermatocytes and early round spermatids. RFX2 also binds X-box motifs in the lamin C2 and Sgy promoters.\",\n      \"method\": \"Competitive band-shift assay, immunoprecipitation with specific antisera, Western blot, immunohistochemistry, in vitro synthesis\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (EMSA, supershift, IHC, in vitro synthesis) establishing homodimer binding and target promoters\",\n      \"pmids\": [\"15229132\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"RFX2 activates the H1t promoter by binding to either X-box element independently for partial activation, but simultaneous binding to both X-box elements (TE1 and TE2) is required for maximal promoter activation.\",\n      \"method\": \"Affinity chromatography, transient expression/reporter assay, site-directed mutagenesis\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reporter assay with double mutagenesis establishes cooperativity requirement\",\n      \"pmids\": [\"15526285\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"RFX2 is the most abundant RFX family member in rat testis, enriched in spermatocyte nuclei where H1t transcription is upregulated; RFX2 levels decrease and RFX1 levels increase in early spermatids where H1t is downregulated, supporting a stage-specific regulatory switch.\",\n      \"method\": \"Western blot, EMSA with antibody supershift, subcellular fractionation across germ cell stages\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — multiple cell-stage comparisons with EMSA, but functional consequence inferred rather than directly tested\",\n      \"pmids\": [\"16676351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"RFX2 binds the H1t X-box in vivo in spermatocytes (ChIP), and cooperates with NF-Y, which binds the adjacent CCAAT-box; NF-Y interacts directly or indirectly with RFX2, and both elements are required for promoter activity.\",\n      \"method\": \"ChIP, EMSA, Western blot, co-expression reporter assay, real-time RT-PCR\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vivo ChIP confirms binding, plus protein-protein interaction (NF-Y/RFX2) and functional mutagenesis of both elements\",\n      \"pmids\": [\"18247329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"A-MYB transcription factor binds MYB binding sites (MBS) in the Rfx2 promoter, occupies the promoter in vivo (ChIP), and is required for Rfx2 expression; Rfx2 expression is virtually eliminated in A-myb knockout testes. RFX2 in turn binds X-boxes in promoters of target genes Adam5, Pdcl2, Spag6, and Alf, and activates the Alf promoter in transfected cells (ChIP and co-transfection confirmed).\",\n      \"method\": \"Electrophoretic gel-shift, ChIP, co-transfection assay, A-myb knockout analysis, immunohistology\",\n      \"journal\": \"BMC developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (EMSA, ChIP, co-transfection, KO) establishing upstream regulation by A-MYB and downstream targets of RFX2\",\n      \"pmids\": [\"20003220\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Rfx2 is expressed in ciliated tissues in Xenopus (neural tube, gastrocoel roof plate, epidermal multi-ciliated cells, otic vesicles, kidneys) and morpholino knockdown results in fewer or truncated cilia and loss of expression of ciliogenic target genes including TTC25; TTC25 is required for ciliogenesis, HH signaling, and left-right patterning.\",\n      \"method\": \"Morpholino knockdown, in situ hybridization, cilia imaging, epistasis\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with specific ciliary phenotype, target gene regulation, and epistasis established in vivo\",\n      \"pmids\": [\"22227339\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Rfx2 is expressed in motile cilia cells in mouse and zebrafish; morpholino knockdown of Rfx2 in zebrafish Kupffer's Vesicle reduces KV cilia length and causes left-right patterning defects including randomization of Nodal pathway genes (southpaw, lefty1, lefty2) and reversal of heart/gut primordia. Rfx2 is also required for ciliogenesis in zebrafish pronephric duct.\",\n      \"method\": \"Morpholino knockdown, in situ hybridization, cilia length measurement, LR patterning analysis, organ-specific transgenic rescue\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — tissue-specific KD with defined molecular (Nodal pathway) and cellular (cilia length) phenotypes, plus transgenic rescue\",\n      \"pmids\": [\"22233545\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Rfx2 genomic occupancy (ChIP-seq) in Xenopus multi-ciliated cells identifies direct target genes controlling ciliogenesis, cilia function, and cell movement; Rfx2 cell-autonomously controls apical surface expansion in nascent multi-ciliated cells as revealed by in vivo cell biological imaging after Rfx2 depletion.\",\n      \"method\": \"ChIP-seq, RNA-seq, morpholino knockdown, in vivo live imaging, bioinformatics\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — genomic ChIP-seq plus in vivo live imaging with loss-of-function, multiple orthogonal approaches\",\n      \"pmids\": [\"24424412\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Rfx2 knockout in mice causes complete male sterility with arrest of spermatid development prior to elongation; arrested spermatids show altered Golgi organization, failure to form an acrosomal cap from proacrosomal vesicles, and complete failure to form the flagellar axoneme. ChIP-seq and RNA-seq identified 139 direct RFX2 target genes during spermiogenesis, enriched in ciliary function genes.\",\n      \"method\": \"Targeted gene knockout, RNA-seq, ChIP-seq, histology, electron microscopy\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — knockout with defined ultrastructural phenotypes, genome-wide direct target identification by ChIP-seq/RNA-seq\",\n      \"pmids\": [\"26162102\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Rfx2 gene trap null mice are viable without neural tube or situs defects but Rfx2gt/gt males are infertile due to spermatid maturation defects at or before round/elongating spermatid stage; lacZ reporter shows Rfx2 expression in ciliated tissues including node, floor plate, and dorsal neural tube.\",\n      \"method\": \"Gene trap knockout, lacZ reporter, RT-PCR, fertility testing, histology\",\n      \"journal\": \"Genesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean null allele with confirmed mRNA loss, defined spermatogenic phenotype\",\n      \"pmids\": [\"26248850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Rfx2 knockout in mice causes arrest of spermatogenesis at an early round spermatid step; round spermatids detach from seminiferous tubules forming multinucleated giant cells that undergo apoptosis; flagellum formation is inhibited at its earliest stage. RNA-seq and ChIP-PCR identified numerous direct RFX2 target genes including cilia-related and testis-specific genes.\",\n      \"method\": \"Knockout mouse, RNA-seq, ChIP-PCR, histology, TUNEL assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — independent replication of knockout phenotype from separate lab, with direct target confirmation by ChIP\",\n      \"pmids\": [\"26853561\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RFX2 binds to the PAF1 promoter (ChIP-qPCR) and activates PAF1 transcription (dual-luciferase assay) in spinal ependymoma cells, thereby promoting tumor stemness; PAF1 overexpression rescues the effects of RFX2 knockdown on stem cell features and malignant progression.\",\n      \"method\": \"ChIP-qPCR, dual-luciferase reporter assay, RFX2 knockdown, in vivo xenograft\",\n      \"journal\": \"Journal of neuro-oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct promoter binding confirmed by ChIP and luciferase, with rescue experiment, but single lab\",\n      \"pmids\": [\"38057505\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ACK1 kinase interacts with RFX2 through its MHR domain (co-immunoprecipitation, mass spectrometry) and competitively inhibits RFX2 ubiquitination by E3 ligase MIB1; ACK1 inhibition promotes MIB1-mediated RFX2 ubiquitination and degradation, thereby relieving RFX2 transcriptional suppression of BNIP3 (confirmed by luciferase reporter and ChIP), leading to mitophagy activation.\",\n      \"method\": \"Co-IP, mass spectrometry, ChIP, luciferase reporter assay, ubiquitination assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (MS, Co-IP, ChIP, reporter, ubiquitination assay) in single study establishing mechanism\",\n      \"pmids\": [\"40715489\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RFX2 binds the RASSF1 promoter (ChIP) and activates RASSF1 transcription (dual-luciferase assay); loss of RFX2 in lung adenocarcinoma downregulates RASSF1, reducing YAP phosphorylation and impairing Hippo signaling, thereby promoting immune escape from CD8+ T cells.\",\n      \"method\": \"ChIP, dual-luciferase reporter assay, RFX2 overexpression, co-culture with CD8+ T cells, in vivo tumor model\",\n      \"journal\": \"Cell division\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — direct promoter binding confirmed by ChIP and luciferase, pathway placement via Hippo signaling, single lab\",\n      \"pmids\": [\"40069841\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SWI/SNF complex component Actl6a maintains expression of rfx2 (and foxj1a) in zebrafish pronephros; depletion of Actl6a reduces chromatin accessibility and SWI/SNF binding at rfx2 locus; overexpression of rfx2 mRNA partially rescues cystic kidney and cilia disassembly in actl6a mutants, placing rfx2 downstream of SWI/SNF in the epigenetic control of ciliogenesis.\",\n      \"method\": \"ATAC-seq, ChIP, morpholino/CRISPR knockout, mRNA rescue, omics analyses in zebrafish\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple omics methods plus genetic rescue, but preprint and single lab\",\n      \"pmids\": [\"bio_10.1101_2025.06.10.658863\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"RFX2 is a winged-helix transcription factor that binds X-box DNA elements as a homodimer to directly activate target gene transcription; it is itself transcriptionally activated by A-MYB in spermatocytes and regulated post-translationally by ACK1-dependent protection from MIB1-mediated ubiquitination; in multi-ciliated cells RFX2 serves as a master coordinator of ciliogenesis (controlling axoneme assembly, cilia function genes) and apical cell morphogenesis, while in spermatids it governs acrosome formation and flagellar axoneme biogenesis through direct regulation of ~139 target genes, and in cancer contexts it suppresses BNIP3 transcription and activates RASSF1/Hippo signaling.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RFX2 is a winged-helix transcription factor that binds X-box DNA motifs as a homodimer to activate transcription of genes governing ciliogenesis, spermiogenesis, and cell identity. RFX2 directly occupies X-box elements in promoters of cilia-related and testis-specific genes, and its cooperative binding to tandem X-box sites—together with cofactors such as NF-Y—is required for maximal promoter activation [PMID:15229132, PMID:18247329, PMID:14743396]. In multi-ciliated cells, RFX2 orchestrates axoneme assembly, cilia function gene expression, and apical surface remodeling, while in spermatids it is essential for acrosome formation and flagellar axoneme biogenesis; Rfx2 knockout mice are viable but exhibit complete male sterility due to spermatid arrest prior to elongation [PMID:24424412, PMID:26162102, PMID:22227339]. RFX2 protein stability is regulated post-translationally by ACK1, which shields RFX2 from MIB1-mediated ubiquitination and proteasomal degradation, linking RFX2 turnover to downstream transcriptional outputs including BNIP3 repression and mitophagy control [PMID:40715489].\",\n  \"teleology\": [\n    {\n      \"year\": 1992,\n      \"claim\": \"Identification of RFX2 as a second RFX family member with conserved DNA-binding features established that X-box recognition is mediated by a multi-gene family, not a single factor.\",\n      \"evidence\": \"Genomic mapping and in situ hybridization to chromosome 19p13\",\n      \"pmids\": [\"1505960\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional assay performed; role inferred from structural similarity to RFX1\", \"No target gene regulation demonstrated\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Biochemical purification and functional assays resolved that RFX2 is the X-box-binding transcription factor in spermatocytes, forming homodimers on the H1t promoter and activating transcription in germinal cells.\",\n      \"evidence\": \"Affinity chromatography from rat testis extracts, EMSA with supershift, reporter assays with mutagenesis, competitive band-shift, immunohistochemistry\",\n      \"pmids\": [\"14743396\", \"15229132\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Homodimerization not structurally resolved\", \"No in vivo occupancy data yet\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Demonstrating that both X-box elements in the H1t promoter must be simultaneously occupied for full activation established a cooperative binding mechanism for RFX2.\",\n      \"evidence\": \"Reporter assays with single and double X-box mutations\",\n      \"pmids\": [\"15526285\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cooperativity mechanism (protein-protein contact vs. chromatin looping) not defined\", \"Single reporter system\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"In vivo ChIP confirmation of RFX2 at the H1t promoter, combined with discovery of NF-Y as a cooperating partner at the adjacent CCAAT-box, revealed a combinatorial transcription logic for spermatocyte-specific gene expression.\",\n      \"evidence\": \"ChIP in spermatocytes, EMSA, co-expression reporter assays\",\n      \"pmids\": [\"18247329\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct physical interaction between RFX2 and NF-Y not confirmed by reciprocal Co-IP or structural data\", \"Whether this cooperativity applies genome-wide is unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Placing RFX2 downstream of A-MYB and identifying additional spermatogenic target genes (Adam5, Pdcl2, Spag6, Alf) established RFX2 as a central node in a transcriptional hierarchy governing spermiogenesis.\",\n      \"evidence\": \"ChIP on Rfx2 and target promoters, A-myb knockout testes showing loss of Rfx2 expression, co-transfection reporter assays\",\n      \"pmids\": [\"20003220\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether A-MYB regulation of Rfx2 is direct in all species not confirmed\", \"Genome-wide target identification not yet performed\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Loss-of-function studies in Xenopus and zebrafish established RFX2 as a master regulator of motile ciliogenesis, required for cilia length, left-right patterning, and expression of ciliogenic target genes like TTC25.\",\n      \"evidence\": \"Morpholino knockdown in Xenopus epidermis and zebrafish Kupffer's vesicle/pronephric duct, cilia imaging, Nodal pathway gene expression analysis, transgenic rescue\",\n      \"pmids\": [\"22227339\", \"22233545\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genetic knockout not yet performed in these organisms\", \"Whether RFX2 acts cell-autonomously in all ciliated tissues not resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Genome-wide ChIP-seq in Xenopus multi-ciliated cells defined the direct RFX2 regulon and revealed a previously unknown cell-autonomous role in apical surface expansion during multi-ciliated cell differentiation.\",\n      \"evidence\": \"ChIP-seq, RNA-seq, morpholino knockdown, in vivo live imaging in Xenopus\",\n      \"pmids\": [\"24424412\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking RFX2 transcriptional targets to apical surface remodeling not defined\", \"Overlap with RFX3 targets not fully delineated\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mouse knockouts from two independent groups demonstrated that RFX2 is dispensable for viability and left-right patterning but absolutely required for spermiogenesis, governing acrosome biogenesis and flagellar axoneme assembly through ~139 direct target genes.\",\n      \"evidence\": \"Targeted knockout and gene-trap null mice, ChIP-seq, RNA-seq, electron microscopy, histology, fertility testing\",\n      \"pmids\": [\"26162102\", \"26248850\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Redundancy with RFX3/RFX4 in ciliated somatic tissues not formally tested\", \"How RFX2 controls Golgi-to-acrosome vesicle trafficking is mechanistically unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"An independent knockout confirmed spermatid arrest and added the observation that RFX2-null spermatids detach from the seminiferous epithelium and undergo apoptosis as multinucleated giant cells, establishing the severity of the maturation block.\",\n      \"evidence\": \"Knockout mouse, RNA-seq, ChIP-PCR, TUNEL assay\",\n      \"pmids\": [\"26853561\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether detachment is a direct consequence of RFX2 target loss or secondary to differentiation failure not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Discovery that ACK1 physically protects RFX2 from MIB1-mediated ubiquitination and degradation established the first post-translational regulatory mechanism for RFX2 protein stability, linking kinase signaling to transcriptional output.\",\n      \"evidence\": \"Co-IP, mass spectrometry, ubiquitination assays, ChIP, luciferase reporter in cancer cell lines\",\n      \"pmids\": [\"40715489\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ACK1 phosphorylates RFX2 or acts solely by competitive binding not determined\", \"Relevance of ACK1–MIB1 axis to normal spermatogenesis or ciliogenesis not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of RASSF1 as a direct RFX2 target in lung adenocarcinoma connected RFX2 transcriptional activity to Hippo pathway regulation and anti-tumor immunity.\",\n      \"evidence\": \"ChIP, dual-luciferase reporter, RFX2 overexpression, co-culture with CD8+ T cells, in vivo tumor model\",\n      \"pmids\": [\"40069841\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding; independent replication needed\", \"Whether RFX2–RASSF1 axis operates in normal tissues unknown\", \"Mechanism of RFX2 downregulation in tumors not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include how RFX2 functionally partitions from RFX3/RFX4 at shared ciliary targets, the structural basis of RFX2 homodimerization and X-box cooperativity, the in vivo relevance of ACK1/MIB1-mediated RFX2 turnover outside cancer cells, and the mechanism by which RFX2 target genes drive acrosome vesicle trafficking.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of RFX2 dimer–DNA complex exists\", \"Redundancy with other RFX paralogs in somatic cilia not genetically dissected\", \"Post-translational regulation in physiological (non-cancer) contexts unexplored\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 2, 5, 6, 9, 10]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 3, 5, 6, 9, 10, 13, 14, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2, 4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0074160\", \"supporting_discovery_ids\": [1, 3, 5, 6, 9, 10, 13, 15]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [7, 8, 9, 10]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [10, 11, 12]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"NF-Y\",\n      \"ACK1\",\n      \"MIB1\",\n      \"A-MYB\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}