{"gene":"CXXC5","run_date":"2026-04-28T17:28:53","timeline":{"discoveries":[{"year":2008,"finding":"CXXC5 interacts with Dishevelled (Dvl) in the cytoplasm and acts as a BMP4-induced inhibitor of canonical Wnt signaling in neural stem cells; CXXC5 overexpression repressed Axin2 levels and attenuated Wnt3a-mediated TOPflash reporter activity, and CXXC5 co-localized and co-immunoprecipitated with Dvl, confirmed by FRET.","method":"Co-immunoprecipitation, FRET, TOPflash reporter assay, RNA interference, overexpression","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, FRET, functional reporter assay, and RNAi knockdown with defined phenotype; replicated in subsequent studies","pmids":["19001364"],"is_preprint":false},{"year":2015,"finding":"CXXC5 acts as a negative-feedback regulator of the Wnt/β-catenin pathway during osteoblast differentiation by Wnt-dependent binding to Dvl; CXXC5-deficient mice have elevated bone mineral density, and a competitor peptide (PTD-DBM) blocking CXXC5-Dvl interaction activated Wnt/β-catenin signaling and osteoblast differentiation.","method":"CXXC5-/- mouse model, competitor peptide disruption of protein-protein interaction, ex vivo calvaria cultures, β-catenin reporter assays","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 — KO mouse with defined bone phenotype, peptide competition, and epistasis placing CXXC5 as Wnt negative feedback via Dvl; strong multi-method evidence","pmids":["25633194"],"is_preprint":false},{"year":2015,"finding":"CXXC5 negatively regulates cutaneous wound healing by interacting with Dvl and suppressing Wnt/β-catenin signaling; CXXC5-/- mice show accelerated wound healing with enhanced keratin 14 and collagen synthesis; disruption of CXXC5-Dvl interaction with PTD-DBM peptide activated β-catenin and collagen production, and combined PTD-DBM and valproic acid treatment synergistically accelerated wound healing.","method":"CXXC5-/- mouse model, peptide competitor (PTD-DBM), in vitro overexpression and siRNA knockdown of CXXC5 in keratinocytes/fibroblasts, β-catenin/α-SMA/collagen I western blotting","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — KO mouse with phenotypic rescue, peptide competition, in vitro loss/gain-of-function; multiple orthogonal methods","pmids":["26056233"],"is_preprint":false},{"year":2017,"finding":"CXXC5 epigenetically recruits the DNA demethylase Tet2 to maintain hypomethylation of CpG islands at the Irf7 locus and other CGI-containing genes in plasmacytoid dendritic cells (pDCs); genetic ablation of CXXC5 results in aberrant CpG methylation of the Irf7 gene, impaired IRF7 expression, and compromised TLR7/9-induced IFN response.","method":"CXXC5 genetic knockout in mice, bisulfite sequencing of CGIs, ChIP for histone modifications, viral infection model (HSV, VSV)","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — KO mouse, bisulfite sequencing, ChIP, and functional infection assay; multiple orthogonal methods in single study","pmids":["28416650"],"is_preprint":false},{"year":2013,"finding":"CXXC5 is a transcriptional activator of Flk-1 (VEGFR2/KDR); it directly binds the Flk-1 promoter region in vitro (DNA binding assay), mutation of the CXXC DNA-binding motif abolished transcriptional activity, and BMP4 induces CXXC5 expression to drive Flk-1 transcription and subsequent endothelial cell differentiation, migration, and vessel formation.","method":"In vitro DNA binding assay, promoter-reporter assays, CXXC5 overexpression/knockdown in mESCs and HUVECs, CXXC5-/- mouse (Matrigel plug angiogenesis), cxxc5 morpholino in zebrafish","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 1-2 — direct DNA binding assay with mutagenesis, reporter assay, KO mouse, and zebrafish morpholino phenotype","pmids":["24136587"],"is_preprint":false},{"year":2016,"finding":"CXXC5 acts as a transcriptional activator for major myelin genes (including MBP) in oligodendrocytes; CXXC5 directly binds the MBP promoter through its CXXC DNA-binding motif, is induced by Wnt/β-catenin signaling, and CXXC5-/- mice exhibit reduced myelin gene expression in the corpus callosum, abnormal myelin structure, and impaired axonal electrical conduction.","method":"CXXC5-/- mouse model, chromatin binding assay (direct binding to MBP promoter), myelination assays, electrophysiology","journal":"Glia","confidence":"High","confidence_rationale":"Tier 2 — direct promoter binding, KO mouse with defined myelin/electrophysiology phenotype; multiple orthogonal methods","pmids":["26462610"],"is_preprint":false},{"year":2017,"finding":"CXXC5 is upregulated in miniaturized hair follicles and arrector pili muscles in balding scalps; CXXC5 negatively regulates hair regrowth and wound-induced hair follicle neogenesis via interaction with Dvl; CXXC5-/- mice display accelerated hair regrowth, and disrupting the CXXC5-Dvl interaction with a competitor peptide activates Wnt/β-catenin and accelerates hair regrowth and hair follicle neogenesis.","method":"CXXC5-/- mouse model, competitor peptide (PTD-DBM), alkaline phosphatase activity assay, wound-induced hair neogenesis model, immunohistochemistry","journal":"The Journal of investigative dermatology","confidence":"High","confidence_rationale":"Tier 2 — KO mouse with phenotypic rescue by peptide competition; multiple functional assays","pmids":["28595998"],"is_preprint":false},{"year":2016,"finding":"Crystal structure of the Dvl1 PDZ domain at 1.76 Å resolution was determined; molecular modeling combining the crystal structure with NMR data revealed the detailed interaction interface between Dvl1 PDZ domain and the CXXC5 peptide.","method":"X-ray crystallography (1.76 Å), NMR solution structure comparison, molecular modeling","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with NMR validation defining binding interface","pmids":["27932247"],"is_preprint":false},{"year":2016,"finding":"Small-molecule inhibitors of the Dvl-CXXC5 interaction activate the Wnt/β-catenin pathway and enhance osteoblast differentiation; NMR titration confirmed direct binding of compound KY-02061 to the Dvl PDZ domain; oral administration of KY-02327 rescued bone loss in an ovariectomized mouse model.","method":"In vitro fluorescence polarization assay for Dvl-CXXC5 interaction, NMR titration, primary osteoblast differentiation assays, ovariectomized mouse model","journal":"EMBO molecular medicine","confidence":"High","confidence_rationale":"Tier 1-2 — NMR-validated direct binding, in vitro and in vivo bone anabolic assays; multiple orthogonal methods","pmids":["26941261"],"is_preprint":false},{"year":2018,"finding":"CXXC5 is required for TGF-β-mediated growth inhibition and apoptosis in hepatocellular carcinoma cells; CXXC5 associates with HDAC1 and competes with Smad2/3 for HDAC1 binding, thereby relieving the inhibitory effect of HDAC1 on TGF-β signaling and forming a positive feedback loop.","method":"RNA-seq (TGF-β target gene identification), CXXC5 knockdown, co-immunoprecipitation (CXXC5-HDAC1-Smad2/3 interactions), cell viability/apoptosis assays","journal":"Journal of molecular cell biology","confidence":"High","confidence_rationale":"Tier 2 — Co-IP demonstrating ternary complex, RNA-seq, loss-of-function with defined apoptosis/cell cycle phenotype","pmids":["29036306"],"is_preprint":false},{"year":2013,"finding":"CXXC5 co-localizes and co-immunoprecipitates with Smad proteins; CXXC5 facilitates Smad3 phosphorylation and Smad4 nuclear translocation, activates TNF-α reporter activity, and induces apoptosis through both extrinsic (caspase-8) and intrinsic (mitochondrial) pathways.","method":"Co-immunoprecipitation, co-localization (fluorescence), FRET, luciferase reporter assay, caspase activity assays, TUNEL/Hoechst staining, flow cytometry","journal":"Current molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and reporter assay with functional apoptosis readout; single lab study","pmids":["23906331"],"is_preprint":false},{"year":2016,"finding":"CXXC5 induces histone H3 lysine 9 methylation at the Cd40lg promoter in CD8+ T cells partly through interaction with the histone methyltransferase SUV39H1, thereby repressing CD40L expression; ThPOK transcription factor suppresses CXXC5 expression to relieve this repression in CD4+ T cells.","method":"Retroviral Thpok transduction, ChIP for H3K9me and H3K27me, CXXC5 transgene overexpression, co-immunoprecipitation (CXXC5-SUV39H1)","journal":"Journal of leukocyte biology","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP, ChIP, and gain-of-function in T cells; single lab study with multiple methods","pmids":["26896487"],"is_preprint":false},{"year":2019,"finding":"CXXC5 (Rinf) in mouse embryonic stem cells binds chromatin at promoters and enhancers of Tet1, Tet2, and pluripotency genes; CXXC5 forms a complex with Nanog, Oct4, Tet1, and Tet2 and facilitates their proper recruitment to regulatory regions; CXXC5 deficiency reduces Tet enzyme and pluripotency gene expression and causes aberrant differentiation.","method":"ChIP-seq (CXXC5 and pluripotency factor binding), co-immunoprecipitation (CXXC5 with Nanog/Oct4/Tet1/Tet2), Rinf-deficient ESCs, RNA-seq","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — ChIP-seq, reciprocal Co-IP, KO ESC phenotype; multiple orthogonal methods","pmids":["31433977"],"is_preprint":false},{"year":2016,"finding":"Zebrafish CXXC5 interacts with SMAD proteins through its ZF-CXXC domain and SMAD MH1 domain; overexpression of CXXC5 increases TGF-β signaling reporter activity; knockdown of cxxc5 causes cardiac looping defects, cardiac dysplasia, and pericardial edema with downregulation of Tgf-β downstream genes (nkx2.5, hand2, has2); co-injection of hand2 mRNA rescues the looping defect.","method":"Co-immunoprecipitation (CXXC5-SMAD interaction), domain mapping, luciferase reporter assay, zebrafish morpholino knockdown, mRNA rescue experiment","journal":"International journal of cardiology","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP with domain mapping, reporter assay, morpholino KD with genetic rescue in zebrafish","pmids":["27077543"],"is_preprint":false},{"year":2009,"finding":"CXXC5 (RINF) is a retinoid-inducible nuclear factor whose expression is upregulated during retinoic acid-induced differentiation of acute promyelocytic leukemia blasts and during cytokine-induced myelopoiesis of normal CD34+ progenitors; shRNA knockdown of CXXC5 impairs normal and tumoral myelopoiesis.","method":"Microarray, shRNA knockdown, CD34+ progenitor differentiation assays, nuclear localization by immunofluorescence","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2-3 — shRNA KD with defined myeloid differentiation phenotype, localization; single lab study","pmids":["19182210"],"is_preprint":false},{"year":2019,"finding":"CXXC5 is a negative regulator of Wnt/β-catenin signaling involved in growth plate senescence; CXXC5 levels gradually increase during growth plate senescence; Cxxc5-/- mice show delayed growth plate senescence and tibial elongation; small molecules (indirubin analogs) disrupting the CXXC5-Dvl interaction elongate tibial length in adolescent mice.","method":"Cxxc5-/- mouse model, in vitro CXXC5-Dvl interaction assay, small molecule screening, tibial length measurement, histological analysis of growth plates","journal":"Life science alliance","confidence":"High","confidence_rationale":"Tier 2 — KO mouse with defined elongation phenotype, small molecule validation, in vitro binding assay","pmids":["30971423"],"is_preprint":false},{"year":2020,"finding":"CXXC5 binds the proximal MYCL1 promoter to repress MYCL1 transcription in quiescent hepatic stellate cells (HSCs); loss of CXXC5 during HSC activation removes CpG methylation and promotes acquisition of acetylated H3K9/H3K27 at the MYCL1 promoter, leading to MYCL1 transactivation and HSC activation.","method":"ChIP (CXXC5 binding to MYCL1 promoter), bisulfite sequencing, H3K9/H3K27 acetylation ChIP, RNA-seq, CXXC5 overexpression/knockdown, MYCL1 knockdown/overexpression epistasis","journal":"Frontiers in cell and developmental biology","confidence":"High","confidence_rationale":"Tier 2 — ChIP, bisulfite sequencing, RNA-seq, and genetic epistasis; multiple orthogonal methods","pmids":["34621736"],"is_preprint":false},{"year":2020,"finding":"CXXC5 binds unmethylated CpG dinucleotides in vitro (demonstrated with recombinant protein); CXXC5 modulates expression of E2-responsive genes and participates in estrogen-driven cellular proliferation, though it lacks an intrinsic transcription activation/repression function.","method":"Recombinant protein production, in vitro CpG binding assay, CXXC5 overexpression/knockdown, E2-stimulation, RNA-seq/microarray for target gene identification","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro binding assay with recombinant protein, validated in cellular context","pmids":["32249801"],"is_preprint":false},{"year":2016,"finding":"CXXC5 expression is directly regulated by E2-ERα through an estrogen response element (ERE) located upstream of the CXXC5 translation start codon; E2-ERα binds this ERE to drive CXXC5 transcription.","method":"Luciferase reporter assays, ERE mutagenesis, ChIP (ERα binding to CXXC5 ERE), RT-PCR/western blot after E2 stimulation","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP, reporter assay with ERE mutagenesis; single lab study","pmids":["27886276"],"is_preprint":false},{"year":2022,"finding":"CXXC5 is a nuclear protein that extensively colocalizes with TET1 and TET2 at CpG islands in mouse ES cells; CXXC5 interacts with TET proteins (5-methylcytosine oxidases); CXXC5 knockout leads to genome-scale reduction of DNA methylation affecting all genomic compartments, suggesting CXXC5 anchors TET proteins at CpG islands to prevent ectopic demethylation.","method":"CXXC5 gene knockout, whole-genome bisulfite sequencing, RNA-seq, co-immunoprecipitation (CXXC5-TET1/TET2), ChIP/genomic colocalization analysis","journal":"Epigenomics","confidence":"High","confidence_rationale":"Tier 1-2 — whole-genome bisulfite sequencing, Co-IP, KO ESC; rigorous and comprehensive multi-method study","pmids":["39585161"],"is_preprint":false},{"year":2022,"finding":"CXXC5 interacts with the CRL4B and NuRD complexes to form a transcriptional repressor complex; ChIP-seq revealed the CXXC5-CRL4B-NuRD complex represses TSC1, activating mTOR signaling and suppressing autophagic cell death in breast cancer cells.","method":"Co-immunoprecipitation (CXXC5 with CRL4B/NuRD components), ChIP-seq, RNA-seq, cell proliferation assays, xenograft tumor model","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — Co-IP, ChIP-seq, KO/KD with defined proliferative/signaling phenotype; multiple orthogonal methods","pmids":["36539038"],"is_preprint":false},{"year":2022,"finding":"CXXC5 (Rinf) and its paralog Idax facilitate expression of Tet enzymes (Tet1/2/3) to promote neural and suppress trophectodermal programs during ESC differentiation; Tet genes are direct targets of CXXC5/Rinf, and combined loss of Idax and Rinf leads to impaired neural differentiation and trophoblast deregulation resembling Tet-deficient phenotypes.","method":"Idax/Rinf double-KO mice, directed neural progenitor and trophoblast differentiation assays, Tet gene expression analysis, embryoid body differentiation, embryonic brain NPC assays","journal":"Stem cell research","confidence":"Medium","confidence_rationale":"Tier 2 — double-KO mouse with defined differentiation phenotype and epistasis with Tet; single study","pmids":["35390758"],"is_preprint":false},{"year":2022,"finding":"CXXC5 (RINF) in immature erythroid cells directly binds the SMAD7 promoter to upregulate SMAD7 expression, thereby inhibiting TGF-β signaling to sustain red blood cell expansion; RINF knockdown reduces SMAD7 expression, accelerates erythroid maturation, and reduces RBC numbers; ectopic SMAD7 rescues the RINF-KD phenotype.","method":"shRNA knockdown in human CD34+ progenitors, erythroid differentiation assays, ChIP (RINF at SMAD7 promoter), 5-hydroxymethylation analysis, SMAD7 ectopic expression rescue","journal":"Haematologica","confidence":"High","confidence_rationale":"Tier 2 — ChIP demonstrating direct promoter binding, KD with genetic rescue, primary human cells; multiple orthogonal methods","pmids":["33241676"],"is_preprint":false},{"year":2023,"finding":"CXXC5 mediates DHT-induced androgenetic alopecia through the PGD2 axis; CXXC5 is required downstream of PGD2 for hair loss induction; Cxxc5-/- mice are resistant to PGD2-induced and DHT-induced hair loss, and disruption of the CXXC5-Dvl interaction with PTD-DBM rescues hair loss.","method":"Cxxc5-/- mouse model, PGD2 topical application, DHT treatment, wound-induced hair neogenesis model, PTD-DBM peptide competition","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with pathway-specific rescue; single lab study","pmids":["36831222"],"is_preprint":false},{"year":2023,"finding":"CXXC5 is overexpressed in AD patient tissues and in 5xFAD transgenic mice, correlating with suppressed Wnt/β-catenin signaling; Cxxc5-/-/5xFAD mice show rescued cognitive deficits, reduced amyloid-β plaques, and attenuated neuroinflammation; small molecule KY19334 (targeting CXXC5-Dvl interaction) significantly improved AD pathogenic phenotypes in 5xFAD mice.","method":"Cxxc5-/- x 5xFAD double mutant mice, KY19334 pharmacological treatment, behavioral tests (cognition), amyloid-β plaque quantification, western blotting, immunostaining","journal":"Pharmacological research","confidence":"Medium","confidence_rationale":"Tier 2 — KO/AD double-mutant mouse with defined cognitive and pathological phenotypes; single lab study","pmids":["37355147"],"is_preprint":false},{"year":2021,"finding":"Proximity interaction mapping of CXXC5 revealed that CXXC5 through its CXXC domain interacts with EMD (emerin), MAZ, and MeCP2; an interplay between CXXC5 and MeCP2 was critical for a subset of CXXC5 target gene expressions, suggesting CXXC5 acts as a nucleation factor for chromatin-regulatory complexes.","method":"Proximity-dependent biotinylation (BioID), mass spectrometry, domain-specific interaction mapping (CXXC domain), siRNA knockdown of MeCP2 with gene expression analysis","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2-3 — BioID/MS proximity mapping with follow-up functional interaction; single lab study","pmids":["34475492"],"is_preprint":false},{"year":2025,"finding":"CXXC5 protein levels are primarily regulated by ubiquitination and degradation through the ubiquitin-proteasome pathway; multiple ubiquitinated lysine residues of CXXC5 were identified by bioUbiquitination approach coupled to sequential immunoprecipitation-mass spectrometry, and these residues contribute to its proteasomal degradation in both MCF-7 and HEK293FT cells.","method":"BioUbiquitination approach, sequential IP-mass spectrometry (ubiquitinated lysine identification), site-directed mutagenesis, proteasome inhibitor treatment, synchronized cell cycle analysis","journal":"Protein science","confidence":"High","confidence_rationale":"Tier 1-2 — MS-based ubiquitination site mapping with mutagenesis validation in two cell lines","pmids":["40371716"],"is_preprint":false}],"current_model":"CXXC5 is a ZF-CXXC domain-containing nuclear protein that binds unmethylated CpG dinucleotides and functions as a context-dependent transcriptional activator or repressor and Wnt/β-catenin pathway inhibitor: in the cytoplasm it interacts with Dishevelled (Dvl) via its Dvl-binding motif to provide negative feedback on Wnt/β-catenin signaling (thereby regulating osteoblast differentiation, hair growth, wound healing, and adipogenesis), while in the nucleus it recruits TET2 to maintain CpG island hypomethylation, associates with HDAC1/Smad complexes to modulate TGF-β signaling, and forms a repressor complex with CRL4B and NuRD to silence target genes; CXXC5 protein levels are controlled by ubiquitin-proteasome degradation."},"narrative":{"teleology":[{"year":2008,"claim":"Establishing that CXXC5 is a cytoplasmic Wnt pathway inhibitor that directly binds Dvl answered the question of how BMP4 cross-talks with Wnt signaling in neural stem cells and identified CXXC5 as a negative regulator acting at the Dvl level.","evidence":"Co-IP, FRET, TOPflash reporter, and RNAi in neural stem cells","pmids":["19001364"],"confidence":"High","gaps":["Structural basis of the CXXC5–Dvl interaction was unknown","In vivo physiological relevance of the CXXC5–Dvl axis was not yet tested"]},{"year":2009,"claim":"Identifying CXXC5 (RINF) as a retinoid-inducible nuclear factor required for myelopoiesis revealed its role in hematopoietic differentiation independent of its Wnt-inhibitory function.","evidence":"Microarray, shRNA knockdown, CD34+ progenitor differentiation assays","pmids":["19182210"],"confidence":"Medium","gaps":["Direct transcriptional targets in myeloid cells were not identified","Whether the myelopoietic role involves CpG binding or Dvl interaction was unclear"]},{"year":2013,"claim":"Demonstrating that CXXC5 directly binds and activates the Flk-1 promoter through its CXXC motif established CXXC5 as a bona fide DNA-binding transcriptional activator, expanding its function beyond cytoplasmic Wnt inhibition to nuclear gene regulation.","evidence":"In vitro DNA binding with CXXC mutagenesis, reporter assays, CXXC5-KO mice, zebrafish morpholino","pmids":["24136587","23906331"],"confidence":"High","gaps":["Genome-wide binding targets were not mapped","Mechanism of transcriptional activation (cofactor recruitment) was unknown"]},{"year":2015,"claim":"Cxxc5-knockout mice with elevated bone density and accelerated wound healing, together with rescue by a Dvl-binding motif competitor peptide (PTD-DBM), established the in vivo physiological significance of the CXXC5–Dvl negative-feedback loop in Wnt-dependent tissue homeostasis.","evidence":"Cxxc5-KO mouse phenotyping (bone, skin wound), PTD-DBM peptide competition, β-catenin reporter assays","pmids":["25633194","26056233"],"confidence":"High","gaps":["Tissue-specific versus systemic contribution of CXXC5 was not delineated","Whether CXXC5's nuclear transcriptional functions also contribute to these phenotypes was untested"]},{"year":2016,"claim":"Multiple studies in 2016 broadened CXXC5's mechanistic repertoire: crystal structure of Dvl1 PDZ domain defined the CXXC5 binding interface; CXXC5 was shown to activate myelin gene (MBP) transcription and regulate myelination in vivo; CXXC5 was found to recruit SUV39H1 to induce H3K9 methylation and repress CD40L in T cells; and small-molecule Dvl–CXXC5 inhibitors rescued osteoporosis in vivo.","evidence":"X-ray crystallography/NMR (Dvl PDZ), CXXC5-KO mouse myelination/electrophysiology, ChIP for H3K9me with Co-IP (SUV39H1), NMR-validated small molecules in ovariectomized mice","pmids":["27932247","26462610","26896487","26941261"],"confidence":"High","gaps":["Full-length CXXC5–Dvl co-crystal structure was not solved","Whether SUV39H1 recruitment depends on the CXXC domain or a distinct interface was unknown","How CXXC5 switches between activator and repressor modes at different loci was unresolved"]},{"year":2017,"claim":"Two advances established CXXC5 as an epigenetic gatekeeper: in pDCs, CXXC5 recruits TET2 to maintain CpG island hypomethylation at Irf7, linking CXXC5 to innate antiviral immunity; in skin, CXXC5 was shown to suppress hair regrowth via Dvl interaction, extending the Wnt-inhibitory axis to hair follicle neogenesis.","evidence":"CXXC5-KO mice with bisulfite sequencing and viral infection (pDCs); CXXC5-KO mice with PTD-DBM peptide in wound-induced hair neogenesis","pmids":["28416650","28595998"],"confidence":"High","gaps":["Whether TET2 recruitment by CXXC5 is direct or mediated by bridging factors was not resolved","Genome-wide scope of CXXC5-dependent CpG island protection was not determined"]},{"year":2018,"claim":"Identifying that CXXC5 competes with Smad2/3 for HDAC1 binding to relieve TGF-β signaling repression established a mechanism by which CXXC5 acts as a positive regulator of TGF-β-mediated growth arrest and apoptosis in hepatocellular carcinoma.","evidence":"Co-IP of CXXC5–HDAC1–Smad ternary interactions, RNA-seq, CXXC5 knockdown with apoptosis assays","pmids":["29036306"],"confidence":"High","gaps":["Stoichiometry and dynamics of the CXXC5–HDAC1–Smad competition were not quantified","Whether this mechanism operates in non-hepatic contexts was untested"]},{"year":2019,"claim":"ChIP-seq in ESCs revealed that CXXC5 (Rinf) occupies promoters and enhancers of Tet1/2 and pluripotency genes, forming a complex with Nanog, Oct4, Tet1, and Tet2, thereby linking CXXC5 to the core pluripotency/epigenetic network and explaining how its loss causes aberrant differentiation.","evidence":"ChIP-seq, reciprocal Co-IP, Rinf-deficient ESCs with RNA-seq","pmids":["31433977"],"confidence":"High","gaps":["Whether CXXC5's DNA binding is instructive for recruiting the pluripotency complex or vice versa was unclear","Functional redundancy with CXXC4/Idax at these loci was not fully resolved"]},{"year":2020,"claim":"Recombinant CXXC5 was shown to directly bind unmethylated CpG dinucleotides in vitro, and CXXC5 was found to directly bind and repress the MYCL1 promoter in quiescent hepatic stellate cells, maintaining CpG methylation and preventing activating histone marks — establishing CXXC5 as a locus-specific transcriptional repressor whose loss triggers gene derepression.","evidence":"Recombinant protein CpG binding assay; ChIP at MYCL1 promoter with bisulfite sequencing and H3K9/K27ac ChIP in hepatic stellate cells","pmids":["32249801","34621736"],"confidence":"High","gaps":["How CXXC5 binding at CpG islands maintains DNA methylation (preventing TET access or recruiting DNMTs) was unresolved","Whether CXXC5 represses MYCL1 through NuRD or other corepressors was not determined"]},{"year":2022,"claim":"Multiple 2022 studies resolved key aspects: CXXC5 colocalizes with TET1/2 genome-wide at CpG islands and its loss causes global DNA hypomethylation (via ectopic TET activity), CXXC5 assembles a CRL4B–NuRD repressor complex to silence TSC1 and activate mTOR in breast cancer, CXXC5 directly activates SMAD7 transcription to sustain erythroid expansion, and combined CXXC5/Idax loss phenocopies TET deficiency in neural differentiation.","evidence":"Whole-genome bisulfite sequencing in CXXC5-KO ESCs; Co-IP with CRL4B/NuRD and ChIP-seq; ChIP at SMAD7 promoter with KD rescue in human CD34+ cells; Idax/Rinf double-KO differentiation assays","pmids":["39585161","36539038","33241676","35390758"],"confidence":"High","gaps":["Whether CXXC5 anchors TET at CpG islands to prevent spreading or actively recruits TET for local demethylation — i.e., the directionality of the CXXC5–TET interaction — remains debated","The mechanism of CRL4B–NuRD recruitment by CXXC5 (direct or bridged) was not mapped","Structural basis for CXXC5's ability to serve as both activator and repressor at different loci is unknown"]},{"year":2025,"claim":"Identification of specific ubiquitinated lysine residues controlling CXXC5 proteasomal degradation established post-translational turnover as a primary mechanism regulating CXXC5 protein levels and hence its functional output.","evidence":"BioUbiquitination–IP–MS with site-directed mutagenesis and proteasome inhibitor treatment in MCF-7 and HEK293FT cells","pmids":["40371716"],"confidence":"High","gaps":["The E3 ubiquitin ligase(s) targeting CXXC5 for degradation were not identified","Whether ubiquitination of CXXC5 is signal-regulated (e.g., Wnt- or TGF-β-dependent) is unknown"]},{"year":null,"claim":"Major unresolved questions include: what determines whether CXXC5 acts as transcriptional activator versus repressor at a given locus; the identity of E3 ligase(s) controlling CXXC5 turnover; a co-crystal structure of full-length CXXC5 with Dvl; and how the cytoplasmic (Dvl-binding) and nuclear (chromatin-regulatory) functions of CXXC5 are coordinated in individual cells.","evidence":"Open questions from the literature","pmids":[],"confidence":"Low","gaps":["No structural model of full-length CXXC5 exists","Signal-dependent partitioning between cytoplasm and nucleus is not characterized","The logic governing activator vs repressor function at specific loci is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[4,5,16,17,22]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[4,5,16,20,22]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,2,9,15]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,4,5,12,14,16,17,19,20,25]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,2,6,8,9,13,15,24]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[3,11,12,16,19]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4,5,14,21,22]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[4,5,16,20,22]}],"complexes":["CRL4B-NuRD repressor complex","Nanog-Oct4-Tet1/2 pluripotency complex"],"partners":["DVL1","TET2","TET1","HDAC1","SUV39H1","MECP2","NANOG","SMAD3"],"other_free_text":[]},"mechanistic_narrative":"CXXC5 is a dual-compartment regulatory protein that functions as a negative-feedback inhibitor of canonical Wnt/β-catenin signaling and as a context-dependent transcriptional regulator coupling CpG methylation status to gene expression. In the cytoplasm, CXXC5 binds Dishevelled (Dvl) via its Dvl-binding motif to suppress Wnt/β-catenin signaling, thereby restraining osteoblast differentiation, hair follicle cycling, cutaneous wound healing, and longitudinal bone growth, as demonstrated by accelerated phenotypes in Cxxc5-knockout mice and rescue by competitor peptides or small molecules that disrupt the CXXC5–Dvl interaction [PMID:25633194, PMID:26056233, PMID:28595998, PMID:30971423]. In the nucleus, CXXC5 binds unmethylated CpG dinucleotides through its ZF-CXXC domain and recruits TET1/TET2 demethylases to CpG islands to maintain local hypomethylation, while also assembling repressive complexes including CRL4B–NuRD and interacting with HDAC1, SUV39H1, and MeCP2 to silence specific target genes such as TSC1 and CD40L [PMID:28416650, PMID:39585161, PMID:36539038, PMID:26896487]. CXXC5 additionally acts as a direct transcriptional activator at promoters of lineage genes including Flk-1 (endothelial differentiation), MBP (myelination), and SMAD7 (erythropoiesis), and its protein levels are controlled by ubiquitin-dependent proteasomal degradation [PMID:24136587, PMID:26462610, PMID:33241676, PMID:40371716]."},"prefetch_data":{"uniprot":{"accession":"Q7LFL8","full_name":"CXXC-type zinc finger protein 5","aliases":["Putative MAPK-activating protein PM08","Putative NF-kappa-B-activating protein 102","Retinoid-inducible nuclear factor","RINF"],"length_aa":322,"mass_kda":33.0,"function":"May indirectly participate in activation of the NF-kappa-B and MAPK pathways. Acts as a mediator of BMP4-mediated modulation of canonical Wnt signaling activity in neural stem cells (By similarity). Required for DNA damage-induced ATM phosphorylation, p53 activation and cell cycle arrest. Involved in myelopoiesis. Transcription factor. Binds to the oxygen responsive element of COX4I2 and represses its transcription under hypoxia conditions (4% oxygen), as well as normoxia conditions (20% oxygen) (PubMed:23303788). May repress COX4I2 transactivation induced by CHCHD2 and RBPJ (PubMed:23303788). Binds preferentially to DNA containing cytidine-phosphate-guanosine (CpG) dinucleotides over CpH (H=A, T, and C), hemimethylated-CpG and hemimethylated-hydroxymethyl-CpG (PubMed:29276034)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q7LFL8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CXXC5","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CXXC5","total_profiled":1310},"omim":[{"mim_id":"618008","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 65; DEE65","url":"https://www.omim.org/entry/618008"},{"mim_id":"616244","title":"COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 2; CHCHD2","url":"https://www.omim.org/entry/616244"},{"mim_id":"612752","title":"CXXC FINGER PROTEIN 5; CXXC5","url":"https://www.omim.org/entry/612752"},{"mim_id":"607976","title":"CYTOCHROME c OXIDASE, SUBUNIT 4I2; COX4I2","url":"https://www.omim.org/entry/607976"},{"mim_id":"147183","title":"RECOMBINATION SIGNAL-BINDING PROTEIN FOR IMMUNOGLOBULIN KAPPA J REGION; RBPJ","url":"https://www.omim.org/entry/147183"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in 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CXXC5 overexpression repressed Axin2 levels and attenuated Wnt3a-mediated TOPflash reporter activity, and CXXC5 co-localized and co-immunoprecipitated with Dvl, confirmed by FRET.\",\n      \"method\": \"Co-immunoprecipitation, FRET, TOPflash reporter assay, RNA interference, overexpression\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, FRET, functional reporter assay, and RNAi knockdown with defined phenotype; replicated in subsequent studies\",\n      \"pmids\": [\"19001364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CXXC5 acts as a negative-feedback regulator of the Wnt/β-catenin pathway during osteoblast differentiation by Wnt-dependent binding to Dvl; CXXC5-deficient mice have elevated bone mineral density, and a competitor peptide (PTD-DBM) blocking CXXC5-Dvl interaction activated Wnt/β-catenin signaling and osteoblast differentiation.\",\n      \"method\": \"CXXC5-/- mouse model, competitor peptide disruption of protein-protein interaction, ex vivo calvaria cultures, β-catenin reporter assays\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with defined bone phenotype, peptide competition, and epistasis placing CXXC5 as Wnt negative feedback via Dvl; strong multi-method evidence\",\n      \"pmids\": [\"25633194\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CXXC5 negatively regulates cutaneous wound healing by interacting with Dvl and suppressing Wnt/β-catenin signaling; CXXC5-/- mice show accelerated wound healing with enhanced keratin 14 and collagen synthesis; disruption of CXXC5-Dvl interaction with PTD-DBM peptide activated β-catenin and collagen production, and combined PTD-DBM and valproic acid treatment synergistically accelerated wound healing.\",\n      \"method\": \"CXXC5-/- mouse model, peptide competitor (PTD-DBM), in vitro overexpression and siRNA knockdown of CXXC5 in keratinocytes/fibroblasts, β-catenin/α-SMA/collagen I western blotting\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with phenotypic rescue, peptide competition, in vitro loss/gain-of-function; multiple orthogonal methods\",\n      \"pmids\": [\"26056233\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CXXC5 epigenetically recruits the DNA demethylase Tet2 to maintain hypomethylation of CpG islands at the Irf7 locus and other CGI-containing genes in plasmacytoid dendritic cells (pDCs); genetic ablation of CXXC5 results in aberrant CpG methylation of the Irf7 gene, impaired IRF7 expression, and compromised TLR7/9-induced IFN response.\",\n      \"method\": \"CXXC5 genetic knockout in mice, bisulfite sequencing of CGIs, ChIP for histone modifications, viral infection model (HSV, VSV)\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse, bisulfite sequencing, ChIP, and functional infection assay; multiple orthogonal methods in single study\",\n      \"pmids\": [\"28416650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"CXXC5 is a transcriptional activator of Flk-1 (VEGFR2/KDR); it directly binds the Flk-1 promoter region in vitro (DNA binding assay), mutation of the CXXC DNA-binding motif abolished transcriptional activity, and BMP4 induces CXXC5 expression to drive Flk-1 transcription and subsequent endothelial cell differentiation, migration, and vessel formation.\",\n      \"method\": \"In vitro DNA binding assay, promoter-reporter assays, CXXC5 overexpression/knockdown in mESCs and HUVECs, CXXC5-/- mouse (Matrigel plug angiogenesis), cxxc5 morpholino in zebrafish\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct DNA binding assay with mutagenesis, reporter assay, KO mouse, and zebrafish morpholino phenotype\",\n      \"pmids\": [\"24136587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CXXC5 acts as a transcriptional activator for major myelin genes (including MBP) in oligodendrocytes; CXXC5 directly binds the MBP promoter through its CXXC DNA-binding motif, is induced by Wnt/β-catenin signaling, and CXXC5-/- mice exhibit reduced myelin gene expression in the corpus callosum, abnormal myelin structure, and impaired axonal electrical conduction.\",\n      \"method\": \"CXXC5-/- mouse model, chromatin binding assay (direct binding to MBP promoter), myelination assays, electrophysiology\",\n      \"journal\": \"Glia\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct promoter binding, KO mouse with defined myelin/electrophysiology phenotype; multiple orthogonal methods\",\n      \"pmids\": [\"26462610\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CXXC5 is upregulated in miniaturized hair follicles and arrector pili muscles in balding scalps; CXXC5 negatively regulates hair regrowth and wound-induced hair follicle neogenesis via interaction with Dvl; CXXC5-/- mice display accelerated hair regrowth, and disrupting the CXXC5-Dvl interaction with a competitor peptide activates Wnt/β-catenin and accelerates hair regrowth and hair follicle neogenesis.\",\n      \"method\": \"CXXC5-/- mouse model, competitor peptide (PTD-DBM), alkaline phosphatase activity assay, wound-induced hair neogenesis model, immunohistochemistry\",\n      \"journal\": \"The Journal of investigative dermatology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with phenotypic rescue by peptide competition; multiple functional assays\",\n      \"pmids\": [\"28595998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Crystal structure of the Dvl1 PDZ domain at 1.76 Å resolution was determined; molecular modeling combining the crystal structure with NMR data revealed the detailed interaction interface between Dvl1 PDZ domain and the CXXC5 peptide.\",\n      \"method\": \"X-ray crystallography (1.76 Å), NMR solution structure comparison, molecular modeling\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with NMR validation defining binding interface\",\n      \"pmids\": [\"27932247\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Small-molecule inhibitors of the Dvl-CXXC5 interaction activate the Wnt/β-catenin pathway and enhance osteoblast differentiation; NMR titration confirmed direct binding of compound KY-02061 to the Dvl PDZ domain; oral administration of KY-02327 rescued bone loss in an ovariectomized mouse model.\",\n      \"method\": \"In vitro fluorescence polarization assay for Dvl-CXXC5 interaction, NMR titration, primary osteoblast differentiation assays, ovariectomized mouse model\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — NMR-validated direct binding, in vitro and in vivo bone anabolic assays; multiple orthogonal methods\",\n      \"pmids\": [\"26941261\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CXXC5 is required for TGF-β-mediated growth inhibition and apoptosis in hepatocellular carcinoma cells; CXXC5 associates with HDAC1 and competes with Smad2/3 for HDAC1 binding, thereby relieving the inhibitory effect of HDAC1 on TGF-β signaling and forming a positive feedback loop.\",\n      \"method\": \"RNA-seq (TGF-β target gene identification), CXXC5 knockdown, co-immunoprecipitation (CXXC5-HDAC1-Smad2/3 interactions), cell viability/apoptosis assays\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP demonstrating ternary complex, RNA-seq, loss-of-function with defined apoptosis/cell cycle phenotype\",\n      \"pmids\": [\"29036306\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"CXXC5 co-localizes and co-immunoprecipitates with Smad proteins; CXXC5 facilitates Smad3 phosphorylation and Smad4 nuclear translocation, activates TNF-α reporter activity, and induces apoptosis through both extrinsic (caspase-8) and intrinsic (mitochondrial) pathways.\",\n      \"method\": \"Co-immunoprecipitation, co-localization (fluorescence), FRET, luciferase reporter assay, caspase activity assays, TUNEL/Hoechst staining, flow cytometry\",\n      \"journal\": \"Current molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and reporter assay with functional apoptosis readout; single lab study\",\n      \"pmids\": [\"23906331\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CXXC5 induces histone H3 lysine 9 methylation at the Cd40lg promoter in CD8+ T cells partly through interaction with the histone methyltransferase SUV39H1, thereby repressing CD40L expression; ThPOK transcription factor suppresses CXXC5 expression to relieve this repression in CD4+ T cells.\",\n      \"method\": \"Retroviral Thpok transduction, ChIP for H3K9me and H3K27me, CXXC5 transgene overexpression, co-immunoprecipitation (CXXC5-SUV39H1)\",\n      \"journal\": \"Journal of leukocyte biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP, ChIP, and gain-of-function in T cells; single lab study with multiple methods\",\n      \"pmids\": [\"26896487\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CXXC5 (Rinf) in mouse embryonic stem cells binds chromatin at promoters and enhancers of Tet1, Tet2, and pluripotency genes; CXXC5 forms a complex with Nanog, Oct4, Tet1, and Tet2 and facilitates their proper recruitment to regulatory regions; CXXC5 deficiency reduces Tet enzyme and pluripotency gene expression and causes aberrant differentiation.\",\n      \"method\": \"ChIP-seq (CXXC5 and pluripotency factor binding), co-immunoprecipitation (CXXC5 with Nanog/Oct4/Tet1/Tet2), Rinf-deficient ESCs, RNA-seq\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-seq, reciprocal Co-IP, KO ESC phenotype; multiple orthogonal methods\",\n      \"pmids\": [\"31433977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Zebrafish CXXC5 interacts with SMAD proteins through its ZF-CXXC domain and SMAD MH1 domain; overexpression of CXXC5 increases TGF-β signaling reporter activity; knockdown of cxxc5 causes cardiac looping defects, cardiac dysplasia, and pericardial edema with downregulation of Tgf-β downstream genes (nkx2.5, hand2, has2); co-injection of hand2 mRNA rescues the looping defect.\",\n      \"method\": \"Co-immunoprecipitation (CXXC5-SMAD interaction), domain mapping, luciferase reporter assay, zebrafish morpholino knockdown, mRNA rescue experiment\",\n      \"journal\": \"International journal of cardiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP with domain mapping, reporter assay, morpholino KD with genetic rescue in zebrafish\",\n      \"pmids\": [\"27077543\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CXXC5 (RINF) is a retinoid-inducible nuclear factor whose expression is upregulated during retinoic acid-induced differentiation of acute promyelocytic leukemia blasts and during cytokine-induced myelopoiesis of normal CD34+ progenitors; shRNA knockdown of CXXC5 impairs normal and tumoral myelopoiesis.\",\n      \"method\": \"Microarray, shRNA knockdown, CD34+ progenitor differentiation assays, nuclear localization by immunofluorescence\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — shRNA KD with defined myeloid differentiation phenotype, localization; single lab study\",\n      \"pmids\": [\"19182210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CXXC5 is a negative regulator of Wnt/β-catenin signaling involved in growth plate senescence; CXXC5 levels gradually increase during growth plate senescence; Cxxc5-/- mice show delayed growth plate senescence and tibial elongation; small molecules (indirubin analogs) disrupting the CXXC5-Dvl interaction elongate tibial length in adolescent mice.\",\n      \"method\": \"Cxxc5-/- mouse model, in vitro CXXC5-Dvl interaction assay, small molecule screening, tibial length measurement, histological analysis of growth plates\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with defined elongation phenotype, small molecule validation, in vitro binding assay\",\n      \"pmids\": [\"30971423\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CXXC5 binds the proximal MYCL1 promoter to repress MYCL1 transcription in quiescent hepatic stellate cells (HSCs); loss of CXXC5 during HSC activation removes CpG methylation and promotes acquisition of acetylated H3K9/H3K27 at the MYCL1 promoter, leading to MYCL1 transactivation and HSC activation.\",\n      \"method\": \"ChIP (CXXC5 binding to MYCL1 promoter), bisulfite sequencing, H3K9/H3K27 acetylation ChIP, RNA-seq, CXXC5 overexpression/knockdown, MYCL1 knockdown/overexpression epistasis\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, bisulfite sequencing, RNA-seq, and genetic epistasis; multiple orthogonal methods\",\n      \"pmids\": [\"34621736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CXXC5 binds unmethylated CpG dinucleotides in vitro (demonstrated with recombinant protein); CXXC5 modulates expression of E2-responsive genes and participates in estrogen-driven cellular proliferation, though it lacks an intrinsic transcription activation/repression function.\",\n      \"method\": \"Recombinant protein production, in vitro CpG binding assay, CXXC5 overexpression/knockdown, E2-stimulation, RNA-seq/microarray for target gene identification\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro binding assay with recombinant protein, validated in cellular context\",\n      \"pmids\": [\"32249801\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CXXC5 expression is directly regulated by E2-ERα through an estrogen response element (ERE) located upstream of the CXXC5 translation start codon; E2-ERα binds this ERE to drive CXXC5 transcription.\",\n      \"method\": \"Luciferase reporter assays, ERE mutagenesis, ChIP (ERα binding to CXXC5 ERE), RT-PCR/western blot after E2 stimulation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, reporter assay with ERE mutagenesis; single lab study\",\n      \"pmids\": [\"27886276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CXXC5 is a nuclear protein that extensively colocalizes with TET1 and TET2 at CpG islands in mouse ES cells; CXXC5 interacts with TET proteins (5-methylcytosine oxidases); CXXC5 knockout leads to genome-scale reduction of DNA methylation affecting all genomic compartments, suggesting CXXC5 anchors TET proteins at CpG islands to prevent ectopic demethylation.\",\n      \"method\": \"CXXC5 gene knockout, whole-genome bisulfite sequencing, RNA-seq, co-immunoprecipitation (CXXC5-TET1/TET2), ChIP/genomic colocalization analysis\",\n      \"journal\": \"Epigenomics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — whole-genome bisulfite sequencing, Co-IP, KO ESC; rigorous and comprehensive multi-method study\",\n      \"pmids\": [\"39585161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CXXC5 interacts with the CRL4B and NuRD complexes to form a transcriptional repressor complex; ChIP-seq revealed the CXXC5-CRL4B-NuRD complex represses TSC1, activating mTOR signaling and suppressing autophagic cell death in breast cancer cells.\",\n      \"method\": \"Co-immunoprecipitation (CXXC5 with CRL4B/NuRD components), ChIP-seq, RNA-seq, cell proliferation assays, xenograft tumor model\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, ChIP-seq, KO/KD with defined proliferative/signaling phenotype; multiple orthogonal methods\",\n      \"pmids\": [\"36539038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CXXC5 (Rinf) and its paralog Idax facilitate expression of Tet enzymes (Tet1/2/3) to promote neural and suppress trophectodermal programs during ESC differentiation; Tet genes are direct targets of CXXC5/Rinf, and combined loss of Idax and Rinf leads to impaired neural differentiation and trophoblast deregulation resembling Tet-deficient phenotypes.\",\n      \"method\": \"Idax/Rinf double-KO mice, directed neural progenitor and trophoblast differentiation assays, Tet gene expression analysis, embryoid body differentiation, embryonic brain NPC assays\",\n      \"journal\": \"Stem cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — double-KO mouse with defined differentiation phenotype and epistasis with Tet; single study\",\n      \"pmids\": [\"35390758\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CXXC5 (RINF) in immature erythroid cells directly binds the SMAD7 promoter to upregulate SMAD7 expression, thereby inhibiting TGF-β signaling to sustain red blood cell expansion; RINF knockdown reduces SMAD7 expression, accelerates erythroid maturation, and reduces RBC numbers; ectopic SMAD7 rescues the RINF-KD phenotype.\",\n      \"method\": \"shRNA knockdown in human CD34+ progenitors, erythroid differentiation assays, ChIP (RINF at SMAD7 promoter), 5-hydroxymethylation analysis, SMAD7 ectopic expression rescue\",\n      \"journal\": \"Haematologica\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP demonstrating direct promoter binding, KD with genetic rescue, primary human cells; multiple orthogonal methods\",\n      \"pmids\": [\"33241676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CXXC5 mediates DHT-induced androgenetic alopecia through the PGD2 axis; CXXC5 is required downstream of PGD2 for hair loss induction; Cxxc5-/- mice are resistant to PGD2-induced and DHT-induced hair loss, and disruption of the CXXC5-Dvl interaction with PTD-DBM rescues hair loss.\",\n      \"method\": \"Cxxc5-/- mouse model, PGD2 topical application, DHT treatment, wound-induced hair neogenesis model, PTD-DBM peptide competition\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with pathway-specific rescue; single lab study\",\n      \"pmids\": [\"36831222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CXXC5 is overexpressed in AD patient tissues and in 5xFAD transgenic mice, correlating with suppressed Wnt/β-catenin signaling; Cxxc5-/-/5xFAD mice show rescued cognitive deficits, reduced amyloid-β plaques, and attenuated neuroinflammation; small molecule KY19334 (targeting CXXC5-Dvl interaction) significantly improved AD pathogenic phenotypes in 5xFAD mice.\",\n      \"method\": \"Cxxc5-/- x 5xFAD double mutant mice, KY19334 pharmacological treatment, behavioral tests (cognition), amyloid-β plaque quantification, western blotting, immunostaining\",\n      \"journal\": \"Pharmacological research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO/AD double-mutant mouse with defined cognitive and pathological phenotypes; single lab study\",\n      \"pmids\": [\"37355147\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Proximity interaction mapping of CXXC5 revealed that CXXC5 through its CXXC domain interacts with EMD (emerin), MAZ, and MeCP2; an interplay between CXXC5 and MeCP2 was critical for a subset of CXXC5 target gene expressions, suggesting CXXC5 acts as a nucleation factor for chromatin-regulatory complexes.\",\n      \"method\": \"Proximity-dependent biotinylation (BioID), mass spectrometry, domain-specific interaction mapping (CXXC domain), siRNA knockdown of MeCP2 with gene expression analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — BioID/MS proximity mapping with follow-up functional interaction; single lab study\",\n      \"pmids\": [\"34475492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CXXC5 protein levels are primarily regulated by ubiquitination and degradation through the ubiquitin-proteasome pathway; multiple ubiquitinated lysine residues of CXXC5 were identified by bioUbiquitination approach coupled to sequential immunoprecipitation-mass spectrometry, and these residues contribute to its proteasomal degradation in both MCF-7 and HEK293FT cells.\",\n      \"method\": \"BioUbiquitination approach, sequential IP-mass spectrometry (ubiquitinated lysine identification), site-directed mutagenesis, proteasome inhibitor treatment, synchronized cell cycle analysis\",\n      \"journal\": \"Protein science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — MS-based ubiquitination site mapping with mutagenesis validation in two cell lines\",\n      \"pmids\": [\"40371716\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CXXC5 is a ZF-CXXC domain-containing nuclear protein that binds unmethylated CpG dinucleotides and functions as a context-dependent transcriptional activator or repressor and Wnt/β-catenin pathway inhibitor: in the cytoplasm it interacts with Dishevelled (Dvl) via its Dvl-binding motif to provide negative feedback on Wnt/β-catenin signaling (thereby regulating osteoblast differentiation, hair growth, wound healing, and adipogenesis), while in the nucleus it recruits TET2 to maintain CpG island hypomethylation, associates with HDAC1/Smad complexes to modulate TGF-β signaling, and forms a repressor complex with CRL4B and NuRD to silence target genes; CXXC5 protein levels are controlled by ubiquitin-proteasome degradation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CXXC5 is a dual-compartment regulatory protein that functions as a negative-feedback inhibitor of canonical Wnt/β-catenin signaling and as a context-dependent transcriptional regulator coupling CpG methylation status to gene expression. In the cytoplasm, CXXC5 binds Dishevelled (Dvl) via its Dvl-binding motif to suppress Wnt/β-catenin signaling, thereby restraining osteoblast differentiation, hair follicle cycling, cutaneous wound healing, and longitudinal bone growth, as demonstrated by accelerated phenotypes in Cxxc5-knockout mice and rescue by competitor peptides or small molecules that disrupt the CXXC5–Dvl interaction [PMID:25633194, PMID:26056233, PMID:28595998, PMID:30971423]. In the nucleus, CXXC5 binds unmethylated CpG dinucleotides through its ZF-CXXC domain and recruits TET1/TET2 demethylases to CpG islands to maintain local hypomethylation, while also assembling repressive complexes including CRL4B–NuRD and interacting with HDAC1, SUV39H1, and MeCP2 to silence specific target genes such as TSC1 and CD40L [PMID:28416650, PMID:39585161, PMID:36539038, PMID:26896487]. CXXC5 additionally acts as a direct transcriptional activator at promoters of lineage genes including Flk-1 (endothelial differentiation), MBP (myelination), and SMAD7 (erythropoiesis), and its protein levels are controlled by ubiquitin-dependent proteasomal degradation [PMID:24136587, PMID:26462610, PMID:33241676, PMID:40371716].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Establishing that CXXC5 is a cytoplasmic Wnt pathway inhibitor that directly binds Dvl answered the question of how BMP4 cross-talks with Wnt signaling in neural stem cells and identified CXXC5 as a negative regulator acting at the Dvl level.\",\n      \"evidence\": \"Co-IP, FRET, TOPflash reporter, and RNAi in neural stem cells\",\n      \"pmids\": [\"19001364\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the CXXC5–Dvl interaction was unknown\",\n        \"In vivo physiological relevance of the CXXC5–Dvl axis was not yet tested\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identifying CXXC5 (RINF) as a retinoid-inducible nuclear factor required for myelopoiesis revealed its role in hematopoietic differentiation independent of its Wnt-inhibitory function.\",\n      \"evidence\": \"Microarray, shRNA knockdown, CD34+ progenitor differentiation assays\",\n      \"pmids\": [\"19182210\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct transcriptional targets in myeloid cells were not identified\",\n        \"Whether the myelopoietic role involves CpG binding or Dvl interaction was unclear\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrating that CXXC5 directly binds and activates the Flk-1 promoter through its CXXC motif established CXXC5 as a bona fide DNA-binding transcriptional activator, expanding its function beyond cytoplasmic Wnt inhibition to nuclear gene regulation.\",\n      \"evidence\": \"In vitro DNA binding with CXXC mutagenesis, reporter assays, CXXC5-KO mice, zebrafish morpholino\",\n      \"pmids\": [\"24136587\", \"23906331\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Genome-wide binding targets were not mapped\",\n        \"Mechanism of transcriptional activation (cofactor recruitment) was unknown\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Cxxc5-knockout mice with elevated bone density and accelerated wound healing, together with rescue by a Dvl-binding motif competitor peptide (PTD-DBM), established the in vivo physiological significance of the CXXC5–Dvl negative-feedback loop in Wnt-dependent tissue homeostasis.\",\n      \"evidence\": \"Cxxc5-KO mouse phenotyping (bone, skin wound), PTD-DBM peptide competition, β-catenin reporter assays\",\n      \"pmids\": [\"25633194\", \"26056233\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Tissue-specific versus systemic contribution of CXXC5 was not delineated\",\n        \"Whether CXXC5's nuclear transcriptional functions also contribute to these phenotypes was untested\"\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Multiple studies in 2016 broadened CXXC5's mechanistic repertoire: crystal structure of Dvl1 PDZ domain defined the CXXC5 binding interface; CXXC5 was shown to activate myelin gene (MBP) transcription and regulate myelination in vivo; CXXC5 was found to recruit SUV39H1 to induce H3K9 methylation and repress CD40L in T cells; and small-molecule Dvl–CXXC5 inhibitors rescued osteoporosis in vivo.\",\n      \"evidence\": \"X-ray crystallography/NMR (Dvl PDZ), CXXC5-KO mouse myelination/electrophysiology, ChIP for H3K9me with Co-IP (SUV39H1), NMR-validated small molecules in ovariectomized mice\",\n      \"pmids\": [\"27932247\", \"26462610\", \"26896487\", \"26941261\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Full-length CXXC5–Dvl co-crystal structure was not solved\",\n        \"Whether SUV39H1 recruitment depends on the CXXC domain or a distinct interface was unknown\",\n        \"How CXXC5 switches between activator and repressor modes at different loci was unresolved\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Two advances established CXXC5 as an epigenetic gatekeeper: in pDCs, CXXC5 recruits TET2 to maintain CpG island hypomethylation at Irf7, linking CXXC5 to innate antiviral immunity; in skin, CXXC5 was shown to suppress hair regrowth via Dvl interaction, extending the Wnt-inhibitory axis to hair follicle neogenesis.\",\n      \"evidence\": \"CXXC5-KO mice with bisulfite sequencing and viral infection (pDCs); CXXC5-KO mice with PTD-DBM peptide in wound-induced hair neogenesis\",\n      \"pmids\": [\"28416650\", \"28595998\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TET2 recruitment by CXXC5 is direct or mediated by bridging factors was not resolved\",\n        \"Genome-wide scope of CXXC5-dependent CpG island protection was not determined\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identifying that CXXC5 competes with Smad2/3 for HDAC1 binding to relieve TGF-β signaling repression established a mechanism by which CXXC5 acts as a positive regulator of TGF-β-mediated growth arrest and apoptosis in hepatocellular carcinoma.\",\n      \"evidence\": \"Co-IP of CXXC5–HDAC1–Smad ternary interactions, RNA-seq, CXXC5 knockdown with apoptosis assays\",\n      \"pmids\": [\"29036306\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Stoichiometry and dynamics of the CXXC5–HDAC1–Smad competition were not quantified\",\n        \"Whether this mechanism operates in non-hepatic contexts was untested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"ChIP-seq in ESCs revealed that CXXC5 (Rinf) occupies promoters and enhancers of Tet1/2 and pluripotency genes, forming a complex with Nanog, Oct4, Tet1, and Tet2, thereby linking CXXC5 to the core pluripotency/epigenetic network and explaining how its loss causes aberrant differentiation.\",\n      \"evidence\": \"ChIP-seq, reciprocal Co-IP, Rinf-deficient ESCs with RNA-seq\",\n      \"pmids\": [\"31433977\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether CXXC5's DNA binding is instructive for recruiting the pluripotency complex or vice versa was unclear\",\n        \"Functional redundancy with CXXC4/Idax at these loci was not fully resolved\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Recombinant CXXC5 was shown to directly bind unmethylated CpG dinucleotides in vitro, and CXXC5 was found to directly bind and repress the MYCL1 promoter in quiescent hepatic stellate cells, maintaining CpG methylation and preventing activating histone marks — establishing CXXC5 as a locus-specific transcriptional repressor whose loss triggers gene derepression.\",\n      \"evidence\": \"Recombinant protein CpG binding assay; ChIP at MYCL1 promoter with bisulfite sequencing and H3K9/K27ac ChIP in hepatic stellate cells\",\n      \"pmids\": [\"32249801\", \"34621736\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How CXXC5 binding at CpG islands maintains DNA methylation (preventing TET access or recruiting DNMTs) was unresolved\",\n        \"Whether CXXC5 represses MYCL1 through NuRD or other corepressors was not determined\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Multiple 2022 studies resolved key aspects: CXXC5 colocalizes with TET1/2 genome-wide at CpG islands and its loss causes global DNA hypomethylation (via ectopic TET activity), CXXC5 assembles a CRL4B–NuRD repressor complex to silence TSC1 and activate mTOR in breast cancer, CXXC5 directly activates SMAD7 transcription to sustain erythroid expansion, and combined CXXC5/Idax loss phenocopies TET deficiency in neural differentiation.\",\n      \"evidence\": \"Whole-genome bisulfite sequencing in CXXC5-KO ESCs; Co-IP with CRL4B/NuRD and ChIP-seq; ChIP at SMAD7 promoter with KD rescue in human CD34+ cells; Idax/Rinf double-KO differentiation assays\",\n      \"pmids\": [\"39585161\", \"36539038\", \"33241676\", \"35390758\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether CXXC5 anchors TET at CpG islands to prevent spreading or actively recruits TET for local demethylation — i.e., the directionality of the CXXC5–TET interaction — remains debated\",\n        \"The mechanism of CRL4B–NuRD recruitment by CXXC5 (direct or bridged) was not mapped\",\n        \"Structural basis for CXXC5's ability to serve as both activator and repressor at different loci is unknown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of specific ubiquitinated lysine residues controlling CXXC5 proteasomal degradation established post-translational turnover as a primary mechanism regulating CXXC5 protein levels and hence its functional output.\",\n      \"evidence\": \"BioUbiquitination–IP–MS with site-directed mutagenesis and proteasome inhibitor treatment in MCF-7 and HEK293FT cells\",\n      \"pmids\": [\"40371716\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The E3 ubiquitin ligase(s) targeting CXXC5 for degradation were not identified\",\n        \"Whether ubiquitination of CXXC5 is signal-regulated (e.g., Wnt- or TGF-β-dependent) is unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Major unresolved questions include: what determines whether CXXC5 acts as transcriptional activator versus repressor at a given locus; the identity of E3 ligase(s) controlling CXXC5 turnover; a co-crystal structure of full-length CXXC5 with Dvl; and how the cytoplasmic (Dvl-binding) and nuclear (chromatin-regulatory) functions of CXXC5 are coordinated in individual cells.\",\n      \"evidence\": \"Open questions from the literature\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of full-length CXXC5 exists\",\n        \"Signal-dependent partitioning between cytoplasm and nucleus is not characterized\",\n        \"The logic governing activator vs repressor function at specific loci is unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [4, 5, 16, 17, 22]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [4, 5, 16, 20, 22]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 2, 9, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 4, 5, 12, 14, 16, 17, 19, 20, 25]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 2, 6, 8, 9, 13, 15, 24]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [3, 11, 12, 16, 19]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4, 5, 14, 21, 22]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [4, 5, 16, 20, 22]}\n    ],\n    \"complexes\": [\n      \"CRL4B-NuRD repressor complex\",\n      \"Nanog-Oct4-Tet1/2 pluripotency complex\"\n    ],\n    \"partners\": [\n      \"DVL1\",\n      \"TET2\",\n      \"TET1\",\n      \"HDAC1\",\n      \"SUV39H1\",\n      \"MECP2\",\n      \"NANOG\",\n      \"SMAD3\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}