{"gene":"CHD5","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2007,"finding":"Chd5 functions as a tumor suppressor that controls proliferation, apoptosis, and senescence via the p19(Arf)/p53 pathway, as demonstrated by chromosome engineering to generate mouse models with gain and loss of the 1p36-corresponding region.","method":"Chromosome engineering (mouse models), in vivo tumor suppression assays, genetic epistasis with p19Arf/p53 pathway","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — chromosome engineering with defined gain/loss models plus pathway epistasis, replicated across multiple models","pmids":["17289567"],"is_preprint":false},{"year":2011,"finding":"CHD5 protein isolated from mouse brain is associated with HDAC2, p66β, MTA3, and RbAp46 in a megadalton NuRD-like complex; CHD5 is predominantly nuclear in neurons and directly binds target neuronal gene promoters as shown by chromatin immunoprecipitation.","method":"Co-immunoprecipitation, microarray expression profiling after CHD5 depletion, chromatin immunoprecipitation (ChIP), subcellular fractionation/immunostaining","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and ChIP in single lab, multiple orthogonal methods","pmids":["21931736"],"is_preprint":false},{"year":2012,"finding":"The tandem PHD fingers of CHD5 specifically recognize the unmodified N-terminus of histone H3; modifications at H3R2, H3K4, H3T3, H3T6, and H3S10 disrupt binding, and the tandem PHD1-2 simultaneously engages two H3 N-termini with 4-11-fold increased affinity compared to individual PHD fingers.","method":"Modified peptide-library platforms (bead and glass slide), NMR, surface plasmon resonance, biochemical binding assays","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal biophysical methods (NMR, SPR, peptide arrays) with quantitative affinity measurements in a single rigorous study","pmids":["22834704"],"is_preprint":false},{"year":2013,"finding":"Chd5 binds the unmodified N-terminus of histone H3 through its tandem PHD domains; PHD mutations that abrogate H3 binding abolish Chd5's ability to inhibit proliferation, transcriptionally modulate target genes, and suppress tumor growth in vivo, establishing that chromatin binding is required for tumor suppression.","method":"PHD domain mutagenesis, genome-wide ChIP-seq, in vivo xenograft tumor assays, neuroblastoma differentiation assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — mutagenesis + ChIP-seq + in vivo functional rescue, multiple orthogonal methods in one study","pmids":["23318260"],"is_preprint":false},{"year":2013,"finding":"Chd5 knockout male mice display defective spermiogenesis with impaired chromatin condensation, abnormal sperm head morphology, and decreased H4 hyperacetylation at stage IX, establishing CHD5 as required for the histone-to-protamine transition during spermatogenesis.","method":"Knockout mouse model, histology, electron microscopy, acidic aniline staining, immunofluorescence for histone modifications","journal":"Mechanisms of development","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with multiple morphological and molecular readouts, replicated by independent study (PMID:24818823)","pmids":["24252660"],"is_preprint":false},{"year":2014,"finding":"CHD5 is a component of the full NuRD transcriptional repressor complex (containing methyl-CpG binding proteins and HDACs); overexpression of CHD5 results in loss of CHD4 protein, suggesting the CHD5/NuRD and CHD4/NuRD complexes are mutually exclusive. CHD5 binds and represses the G2/M checkpoint gene WEE1, and a catalytically inactive CHD5 mutant associates with NuRD but fails to repress transcription.","method":"Biochemical purification of human CHD5 complex, co-immunoprecipitation, CHD5 re-introduction into neuroblastoma cells, catalytically inactive mutant analysis, gene expression assays","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — purification of endogenous complex, active-site mutagenesis showing loss of transcriptional repression, target gene identification, single lab with multiple orthogonal methods","pmids":["25247294"],"is_preprint":false},{"year":2014,"finding":"CHD5 is a chromatin remodeling ATPase that exposes nucleosomal DNA at discrete positions (nucleosome unwrapping) in an ATP hydrolysis-dependent manner; continued ATP hydrolysis is not required to maintain the remodeled state, and this activity is distinct from ACF and BRG1, which reposition nucleosomes. CHD4 shows strong ATPase activity but does not unwrap nucleosomes as efficiently as CHD5.","method":"In vitro nucleosome remodeling assay, ATPase assay, comparison with related remodeling ATPases","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical reconstitution of enzymatic activity with mechanistic dissection, single lab","pmids":["24923445"],"is_preprint":false},{"year":2014,"finding":"Chd5 orchestrates a cascade of molecular events during spermiogenesis required for histone removal and replacement: H4 hyperacetylation, histone variant expression, nucleosome eviction, DNA damage repair, and expression of transition proteins (Tnp1/Tnp2) and protamines (Prm1/2). Chd5 deficiency leads to defective sperm chromatin compaction and male infertility.","method":"Chd5 knockout mouse, spermiogenesis phenotyping, molecular analysis of histone modifications, gene expression (mRNA), chromatin compaction assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with multiple orthogonal molecular readouts, replicates and extends findings from PMID:24252660","pmids":["24818823"],"is_preprint":false},{"year":2014,"finding":"CHD5 is expressed during neuronal differentiation in the developing mouse brain; Chd5 subcellular localization switches from cytoplasm to nucleus during mid-gestation, and high nuclear levels are maintained in differentiated adult neurons.","method":"Immunostaining of endogenous Chd5 protein across developmental time points in mouse brain sections, subcellular localization analysis","journal":"Gene expression patterns : GEP","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment across multiple developmental stages, single lab, no functional manipulation linked to localization switch","pmids":["24120991"],"is_preprint":false},{"year":2014,"finding":"CHD5 is a nucleosome-stimulated ATPase (demonstrated with recombinant zebrafish Chd5 protein in vitro); knockdown of Chd5 during zebrafish embryogenesis causes craniofacial development defects and impaired dopaminergic amacrine cell differentiation, establishing a conserved role in neuronal differentiation.","method":"In vitro nucleosome remodeling/ATPase assay with recombinant protein, morpholino knockdown in zebrafish, neural marker expression analysis","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro ATPase assay plus in vivo KD phenotype, single lab, zebrafish ortholog","pmids":["26092436"],"is_preprint":false},{"year":2014,"finding":"CHD5 is clearly associated with all canonical NuRD components—MTA1/2, GATAD2A, HDAC1/2, RBBP4/7, and MBD2/3—as determined by immunoprecipitation from neuroblastoma cell nuclear extracts and confirmed by MS/MS analysis. GST-FOG1 pulldown also identified NuRD components associated with CHD5.","method":"Co-immunoprecipitation from endogenous and V5-tagged CHD5 cells, GST-FOG1 pulldown, MS/MS mass spectrometry, Western blotting","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus GST pulldown plus MS/MS confirmation, multiple orthogonal methods in a single focused study","pmids":["25825869"],"is_preprint":false},{"year":2015,"finding":"Chd5 represses murine endogenous retrovirus-L (MuERV-L/MERVL) retrotransposons in mouse embryonic stem cells by regulating H3K27me3 modification and histone H3.1/H3.2 incorporation.","method":"CRISPR-Cas9 knockout of Chd5 locus in mESCs, analysis of MERVL expression, ChIP for H3K27me3, histone variant analysis","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean CRISPR KO with molecular readouts for specific chromatin modifications and retrotransposon expression, single lab","pmids":["26359639"],"is_preprint":false},{"year":2014,"finding":"CHD5 expression in spermatogenesis is restricted to post-meiotic round spermatids with a maximum at stage VIII, shows complementary expression with CHD3/4, and CHD5 co-localizes with macroH2A1.2 at centromeres and part of the Y chromosome in post-meiotic cells, suggesting a role in sex chromosome chromatin regulation. CHD5 was demonstrated to be a nucleosome-stimulated ATPase in vitro.","method":"Immunostaining of mouse testis sections across spermatogenic stages, co-localization with macroH2A1.2, in vitro ATPase assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiments with functional ATPase assay, single lab, two orthogonal methods","pmids":["24849318"],"is_preprint":false},{"year":2012,"finding":"The lysine demethylase JMJD2A/KDM4A transcriptionally represses CHD5, blocking Ras-induced upregulation of CHD5 and thereby reducing p53 pathway activity to promote cellular transformation.","method":"Gene expression analysis after JMJD2A overexpression/depletion, oncogenic Ras cooperation assays, cellular senescence assays, p53 pathway reporter assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — CHD5 identified as a transcriptional target of JMJD2A with functional pathway consequence, single lab, limited direct mechanistic detail on CHD5 itself","pmids":["23168260"],"is_preprint":false},{"year":2012,"finding":"miR-211 directly binds the 3'-UTR of CHD5 mRNA, causing ~50% reduction in CHD5 protein level and promoting colorectal cancer cell proliferation, migration, and tumor growth; enforced miR-211 expression alters p53 pathway proteins (MDM2, Bcl-2, Bcl-xL, Bax).","method":"Lentiviral miR-211 overexpression, luciferase 3'-UTR reporter assay, Western blot, xenograft tumor assay, flow cytometry","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — 3'-UTR luciferase assay confirming direct miRNA-mRNA interaction, functional assays in vitro and in vivo, single lab","pmids":["22235338"],"is_preprint":false},{"year":2016,"finding":"CHD5 acts as a transcriptional repressor of multiple oncogenes (MYC, MDM2, STAT3, CCND1, YAP1), epigenetic master genes (Bmi-1, EZH2, JMJD2C), and EMT/stem cell markers (SNAI1, FN1, OCT4) in renal cell carcinoma cells; ChIP assays confirmed direct CHD5 binding to target gene promoters.","method":"Ectopic CHD5 expression in RCC cells, qRT-PCR, Western blot, chromatin immunoprecipitation (ChIP), clonogenicity/migration/invasion assays","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP confirming direct promoter binding plus functional gene expression changes, single lab","pmids":["26943038"],"is_preprint":false},{"year":2015,"finding":"CHD5 and EZH2 mutually repress each other's transcription: CHD5 is epigenetically silenced by PRC2-mediated H3K27me3 in HCC cells, and overexpression of CHD5 in turn represses EZH2 and activates PRC2 target genes p16 and p21. ChIP and luciferase reporter assays confirmed reciprocal promoter binding.","method":"ChIP for H3K27me3, ChIP for CHD5 and EZH2 binding to respective promoters, luciferase reporter assays, gain-of-function CHD5 expression","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and luciferase reporter assays with multiple orthogonal approaches, single lab","pmids":["26517514"],"is_preprint":false},{"year":2015,"finding":"CHD5 upregulation is induced by retinoic acid (13cRA) treatment in a time- and dose-dependent manner only in neuroblastoma cell lines that subsequently undergo neuronal differentiation; NGF/TrkA signaling also induces CHD5 upregulation and differentiation, placing CHD5 downstream of TrkA signaling.","method":"13cRA treatment of NB cell lines, qRT-PCR, Western blot, pan-TRK inhibitor blockade, TrkA transfection experiments, morphological differentiation assessment","journal":"Molecular cancer","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — genetic pathway placement by pharmacological inhibition and receptor expression experiments, single lab, multiple cell lines","pmids":["26245651"],"is_preprint":false},{"year":2021,"finding":"CHD5 forced expression in neuroblastoma cells with 1p loss inhibits anchorage-independent growth, migration, and invasion in vitro, and delays/reduces bone marrow and liver metastasis in vivo. Genome-wide mRNA sequencing revealed upregulation of the metastasis suppressor PLCL1; knockdown of PLCL1 or p53 reversed CHD5-induced inhibition of invasion, placing PLCL1 and p53 as downstream effectors of CHD5 metastasis suppression.","method":"Forced CHD5 expression in NB cell lines, in vitro migration/invasion/anchorage-independent growth assays, intravenous xenograft mouse model, genome-wide RNA-seq, PLCL1 and p53 knockdown epistasis experiments","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis experiments with RNA-seq and in vivo validation, single lab","pmids":["34789839"],"is_preprint":false},{"year":2023,"finding":"Chd5 promotes neuronal differentiation by directing stepwise transcriptional changes: during early neurogenesis, Chd5 promotes expression of the proneural transcription factor Six3, which in turn represses Wnt5a (a non-canonical Wnt ligand required for neuronal maturation), establishing a Chd5→Six3→Wnt5a regulatory axis critical for lineage specification.","method":"Transcriptional profiling of Chd5-deficient mouse cells at early and late neuronal differentiation stages, genetic epistasis using Chd5 knockout mouse model","journal":"Stem cells (Dayton, Ohio)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO model with transcriptional profiling establishing pathway hierarchy, single lab","pmids":["36636025"],"is_preprint":false},{"year":2008,"finding":"CHD5 promoter CpG island hypermethylation silences CHD5 expression in cancer; CHD5 is the only CHD family member (CHD1-9) whose promoter is hypermethylated in human cancer cell lines and primary tumors (gliomas, colon, breast carcinomas). Treatment with DNA demethylating agent restores CHD5 mRNA expression.","method":"Methylation profiling of CHD family members in cancer lines and primary tumors, RT-qPCR, 5-aza-2'-deoxycytidine demethylation treatment","journal":"Epigenetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — systematic comparison across all CHD family members with functional demethylation rescue, single lab","pmids":["18698156"],"is_preprint":false},{"year":2013,"finding":"The transcription factor AP2 activates CHD5 promoter activity; CHD5 promoter methylation represses AP2 recruitment and reduces promoter activity. Treatment with DNA methyltransferase inhibitor DAC increases AP2 recruitment to the CHD5 promoter.","method":"Chromatin immunoprecipitation (ChIP-PCR), luciferase reporter assay, AP2 overexpression, DAC treatment","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, ChIP and reporter assay only, limited mechanistic dissection","pmids":["24454811"],"is_preprint":false}],"current_model":"CHD5 is an ATP-dependent chromatin remodeling ATPase that assembles into a NuRD-type repressor complex (with HDAC1/2, MTA1/2, GATAD2A, RBBP4/7, MBD2/3), binds the unmodified N-terminus of histone H3 via its tandem PHD fingers, remodels nucleosomes by DNA unwrapping, and functions as a tumor suppressor by transcriptionally repressing target genes (including WEE1 and oncogenes) and activating p19Arf/p53 pathway-dependent proliferation control, apoptosis, and senescence; in the germline it orchestrates the histone-to-protamine chromatin remodeling cascade essential for spermiogenesis, and in the developing brain it promotes neuronal differentiation through a Chd5→Six3→Wnt5a transcriptional axis."},"narrative":{"mechanistic_narrative":"CHD5 is an ATP-dependent chromatin-remodeling ATPase that functions as a tumor suppressor and a master regulator of cell-fate transitions in the nervous system and germline [PMID:17289567, PMID:23318260]. Biochemically, CHD5 is a nucleosome-stimulated ATPase that remodels nucleosomes by exposing nucleosomal DNA (unwrapping) in an ATP-hydrolysis-dependent manner, an activity distinct from the nucleosome-repositioning enzymes ACF and BRG1 and more efficient at unwrapping than its paralog CHD4 [PMID:24923445, PMID:24849318]. Its tandem PHD fingers read the unmodified N-terminus of histone H3, engaging two H3 tails simultaneously with enhanced affinity, while modifications at H3R2, H3K4, H3T3, H3T6, and H3S10 abolish binding [PMID:22834704]. CHD5 assembles into a megadalton NuRD-type repressor complex containing HDAC1/2, MTA1/2, GATAD2A, RBBP4/7, and MBD2/3, and its incorporation appears mutually exclusive with CHD4 [PMID:21931736, PMID:25825869, PMID:25247294]. Chromatin engagement is essential for function: PHD mutations that abolish H3 binding eliminate CHD5's ability to inhibit proliferation, modulate target genes, and suppress tumors, and a catalytically inactive mutant still joins NuRD but fails to repress transcription [PMID:23318260, PMID:25247294]. Through direct promoter binding, CHD5 represses the G2/M regulator WEE1 and a broad oncogenic program (MYC, MDM2, STAT3, CCND1, YAP1, EZH2, Bmi-1) while controlling proliferation, apoptosis, and senescence via the p19Arf/p53 pathway [PMID:25247294, PMID:26943038, PMID:17289567]; its tumor-suppressor output extends to metastasis through a CHD5→PLCL1/p53 axis [PMID:34789839]. In the developing brain CHD5 drives neuronal differentiation, in part via a Chd5→Six3→Wnt5a transcriptional cascade [PMID:36636025], and in the male germline it orchestrates the histone-to-protamine transition required for sperm chromatin condensation [PMID:24252660, PMID:24818823]. CHD5 is itself silenced in cancer by promoter CpG hypermethylation, PRC2-mediated H3K27me3, and post-transcriptional repression by miR-211 [PMID:18698156, PMID:26517514, PMID:22235338].","teleology":[{"year":2007,"claim":"Established CHD5 as a genuine tumor suppressor acting through a defined pathway, answering whether the 1p36 candidate gene had causal anti-tumor activity in vivo.","evidence":"Chromosome engineering of mouse gain/loss models with p19Arf/p53 pathway epistasis","pmids":["17289567"],"confidence":"High","gaps":["Did not define the molecular/enzymatic activity of CHD5","Direct gene targets not yet identified"]},{"year":2008,"claim":"Explained how CHD5 is inactivated in human tumors without mutation, showing promoter CpG hypermethylation uniquely silences CHD5 among CHD family members.","evidence":"Methylation profiling of CHD1-9 in cancer lines/primary tumors with 5-aza demethylation rescue","pmids":["18698156"],"confidence":"Medium","gaps":["Correlative across tumor types","Did not address downstream consequences of silencing on specific targets"]},{"year":2011,"claim":"Provided the first biochemical picture of CHD5 as a NuRD-like complex member that binds neuronal gene promoters, linking it to transcriptional repression in neurons.","evidence":"Co-IP, ChIP, expression profiling and fractionation from mouse brain","pmids":["21931736"],"confidence":"Medium","gaps":["Partial complex composition only","No catalytic or remodeling mechanism defined"]},{"year":2012,"claim":"Defined the histone reader specificity of CHD5, showing tandem PHD fingers recognize unmodified H3 N-termini and engage two tails cooperatively.","evidence":"Peptide arrays, NMR, SPR and quantitative binding assays","pmids":["22834704"],"confidence":"High","gaps":["In vitro peptide system, not nucleosomal context","Did not link binding to in vivo function"]},{"year":2012,"claim":"Identified upstream regulators of CHD5, placing it under control of JMJD2A/KDM4A and miR-211 to connect CHD5 loss to the p53 pathway and tumor growth.","evidence":"JMJD2A gain/loss with Ras cooperation assays; miR-211 3'-UTR luciferase reporter and xenograft assays","pmids":["23168260","22235338"],"confidence":"Medium","gaps":["Regulatory effects on CHD5 are indirect/post-transcriptional","p53 pathway effects inferred from downstream proteins"]},{"year":2013,"claim":"Proved that chromatin binding is mechanistically required for tumor suppression by linking PHD-mediated H3 reading to all functional outputs.","evidence":"PHD mutagenesis, genome-wide ChIP-seq, xenograft and neuroblastoma differentiation assays","pmids":["23318260"],"confidence":"High","gaps":["Did not resolve the remodeling enzymology","Full target gene network only partially defined"]},{"year":2013,"claim":"Began to dissect transcriptional control of CHD5 itself, showing AP2 activates the CHD5 promoter in a methylation-sensitive manner.","evidence":"ChIP-PCR, luciferase reporter, AP2 overexpression, DAC treatment","pmids":["24454811"],"confidence":"Low","gaps":["Limited mechanistic dissection, ChIP and reporter only","No in vivo validation"]},{"year":2014,"claim":"Resolved the enzymatic mechanism, defining CHD5 as a nucleosome-stimulated ATPase that unwraps rather than repositions nucleosomes, distinguishing it from ACF, BRG1, and CHD4.","evidence":"In vitro nucleosome remodeling and ATPase assays with comparison to related ATPases; recombinant zebrafish protein assays","pmids":["24923445","26092436","24849318"],"confidence":"High","gaps":["Structural basis of unwrapping not determined","Physiological consequences of unwrapping vs repositioning unclear"]},{"year":2014,"claim":"Completed the NuRD complex membership map and tied catalytic activity to repression, showing CHD5/NuRD represses WEE1 and that catalytic activity (not complex assembly) is required for repression.","evidence":"Endogenous complex purification, reciprocal Co-IP, GST-FOG1 pulldown, MS/MS, catalytically inactive mutant analysis","pmids":["25247294","25825869"],"confidence":"High","gaps":["Mechanism of CHD5/CHD4 mutual exclusivity unresolved","Full target gene repertoire not exhaustively defined"]},{"year":2014,"claim":"Established a germline function, showing CHD5 is required for the histone-to-protamine transition and sperm chromatin condensation.","evidence":"Chd5 knockout mice with histology, EM, histone-modification immunofluorescence and gene expression of transition proteins/protamines","pmids":["24252660","24818823","24849318"],"confidence":"High","gaps":["Direct chromatin targets in spermatids not mapped","Mechanistic link from H4 hyperacetylation to nucleosome eviction incomplete"]},{"year":2014,"claim":"Connected CHD5 expression to neuronal differentiation programs and placed it downstream of retinoic acid and NGF/TrkA signaling.","evidence":"Developmental immunostaining in mouse brain; 13cRA and TrkA induction with pan-TRK blockade in neuroblastoma lines","pmids":["24120991","26245651"],"confidence":"Medium","gaps":["Cause of cytoplasm-to-nucleus localization switch unknown","Mechanism linking TrkA signaling to CHD5 induction undefined"]},{"year":2015,"claim":"Broadened CHD5's repressive target spectrum and revealed reciprocal antagonism with PRC2/EZH2 and silencing by H3K27me3.","evidence":"ChIP, luciferase reporters and gain-of-function expression in RCC and HCC cells; CRISPR KO mESC analysis of MERVL/H3K27me3","pmids":["26943038","26517514","26359639"],"confidence":"Medium","gaps":["Single-lineage observations not generalized","Direct vs indirect repression of each target not fully separated"]},{"year":2021,"claim":"Extended tumor suppression beyond proliferation to metastasis, identifying a CHD5→PLCL1/p53 effector axis.","evidence":"Forced expression in neuroblastoma, RNA-seq, in vivo metastasis model, PLCL1/p53 knockdown epistasis","pmids":["34789839"],"confidence":"Medium","gaps":["Whether PLCL1 is a direct CHD5 target not established","Mechanism of p53 cooperation in metastasis unresolved"]},{"year":2023,"claim":"Defined a transcriptional hierarchy for CHD5 in neurogenesis, establishing the Chd5→Six3→Wnt5a axis for neuronal lineage specification.","evidence":"Transcriptional profiling and genetic epistasis in Chd5 knockout mouse cells across differentiation stages","pmids":["36636025"],"confidence":"Medium","gaps":["Whether Six3 is a direct chromatin target of CHD5 not shown","NuRD requirement for this axis not tested"]},{"year":null,"claim":"How CHD5's nucleosome-unwrapping activity, PHD-mediated H3 reading, and NuRD assembly are integrated into target-gene selection across distinct tissues remains undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of CHD5 on a nucleosome","Determinants of tissue-specific target selection unknown","Basis for CHD5 vs CHD4 NuRD partitioning unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[6,9,12]},{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[2,3]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[5,15,16]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[6,9]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,8]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[12]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2,6,11]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[5,15,19]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,18,20]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[4,7]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[9,19]}],"complexes":["NuRD complex"],"partners":["HDAC1","HDAC2","MTA1","MTA2","GATAD2A","RBBP4","MBD2","MBD3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O00258","full_name":"Guided entry of tail-anchored proteins factor 1","aliases":["Congenital heart disease 5 protein","Tail-anchored protein insertion receptor WRB","Tryptophan-rich basic protein"],"length_aa":174,"mass_kda":19.8,"function":"Required for the post-translational delivery of tail-anchored (TA) proteins to the endoplasmic reticulum (ER) (PubMed:21444755, PubMed:23041287, PubMed:24392163, PubMed:27226539). Together with CAMLG/GET2, acts as a membrane receptor for soluble GET3/TRC40, which recognizes and selectively binds the transmembrane domain of TA proteins in the cytosol (PubMed:21444755, PubMed:23041287, PubMed:24392163, PubMed:27226539). Required to ensure correct topology and ER insertion of CAMLG (PubMed:31417168, PubMed:32187542)","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/O00258/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CHD5","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/CHD5","total_profiled":1310},"omim":[{"mim_id":"619873","title":"PARENTI-MIGNOT NEURODEVELOPMENTAL SYNDROME; PMNDS","url":"https://www.omim.org/entry/619873"},{"mim_id":"616114","title":"CHROMODOMAIN HELICASE DNA-BINDING PROTEIN 6; CHD6","url":"https://www.omim.org/entry/616114"},{"mim_id":"614997","title":"GATA ZINC FINGER DOMAIN-CONTAINING PROTEIN 2A; GATAD2A","url":"https://www.omim.org/entry/614997"},{"mim_id":"610771","title":"CHROMODOMAIN HELICASE DNA-BINDING PROTEIN 5; CHD5","url":"https://www.omim.org/entry/610771"},{"mim_id":"607872","title":"CHROMOSOME 1p36 DELETION SYNDROME, DISTAL","url":"https://www.omim.org/entry/607872"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear speckles","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"brain","ntpm":80.2},{"tissue":"pituitary 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is a tumor suppressor at human 1p36.","date":"2007","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/17289567","citation_count":282,"is_preprint":false},{"pmid":"18577749","id":"PMC_18577749","title":"CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.","date":"2008","source":"Journal of the National Cancer Institute","url":"https://pubmed.ncbi.nlm.nih.gov/18577749","citation_count":145,"is_preprint":false},{"pmid":"12592387","id":"PMC_12592387","title":"CHD5, a new member of the chromodomain gene family, is preferentially expressed in the nervous system.","date":"2003","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/12592387","citation_count":140,"is_preprint":false},{"pmid":"23168260","id":"PMC_23168260","title":"JMJD2A promotes cellular transformation by blocking cellular senescence through transcriptional repression of the tumor suppressor CHD5.","date":"2012","source":"Cell 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controls proliferation, apoptosis, and senescence via the p19(Arf)/p53 pathway, as demonstrated by chromosome engineering to generate mouse models with gain and loss of the 1p36-corresponding region.\",\n      \"method\": \"Chromosome engineering (mouse models), in vivo tumor suppression assays, genetic epistasis with p19Arf/p53 pathway\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — chromosome engineering with defined gain/loss models plus pathway epistasis, replicated across multiple models\",\n      \"pmids\": [\"17289567\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"CHD5 protein isolated from mouse brain is associated with HDAC2, p66β, MTA3, and RbAp46 in a megadalton NuRD-like complex; CHD5 is predominantly nuclear in neurons and directly binds target neuronal gene promoters as shown by chromatin immunoprecipitation.\",\n      \"method\": \"Co-immunoprecipitation, microarray expression profiling after CHD5 depletion, chromatin immunoprecipitation (ChIP), subcellular fractionation/immunostaining\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and ChIP in single lab, multiple orthogonal methods\",\n      \"pmids\": [\"21931736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The tandem PHD fingers of CHD5 specifically recognize the unmodified N-terminus of histone H3; modifications at H3R2, H3K4, H3T3, H3T6, and H3S10 disrupt binding, and the tandem PHD1-2 simultaneously engages two H3 N-termini with 4-11-fold increased affinity compared to individual PHD fingers.\",\n      \"method\": \"Modified peptide-library platforms (bead and glass slide), NMR, surface plasmon resonance, biochemical binding assays\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal biophysical methods (NMR, SPR, peptide arrays) with quantitative affinity measurements in a single rigorous study\",\n      \"pmids\": [\"22834704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Chd5 binds the unmodified N-terminus of histone H3 through its tandem PHD domains; PHD mutations that abrogate H3 binding abolish Chd5's ability to inhibit proliferation, transcriptionally modulate target genes, and suppress tumor growth in vivo, establishing that chromatin binding is required for tumor suppression.\",\n      \"method\": \"PHD domain mutagenesis, genome-wide ChIP-seq, in vivo xenograft tumor assays, neuroblastoma differentiation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — mutagenesis + ChIP-seq + in vivo functional rescue, multiple orthogonal methods in one study\",\n      \"pmids\": [\"23318260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Chd5 knockout male mice display defective spermiogenesis with impaired chromatin condensation, abnormal sperm head morphology, and decreased H4 hyperacetylation at stage IX, establishing CHD5 as required for the histone-to-protamine transition during spermatogenesis.\",\n      \"method\": \"Knockout mouse model, histology, electron microscopy, acidic aniline staining, immunofluorescence for histone modifications\",\n      \"journal\": \"Mechanisms of development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with multiple morphological and molecular readouts, replicated by independent study (PMID:24818823)\",\n      \"pmids\": [\"24252660\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CHD5 is a component of the full NuRD transcriptional repressor complex (containing methyl-CpG binding proteins and HDACs); overexpression of CHD5 results in loss of CHD4 protein, suggesting the CHD5/NuRD and CHD4/NuRD complexes are mutually exclusive. CHD5 binds and represses the G2/M checkpoint gene WEE1, and a catalytically inactive CHD5 mutant associates with NuRD but fails to repress transcription.\",\n      \"method\": \"Biochemical purification of human CHD5 complex, co-immunoprecipitation, CHD5 re-introduction into neuroblastoma cells, catalytically inactive mutant analysis, gene expression assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — purification of endogenous complex, active-site mutagenesis showing loss of transcriptional repression, target gene identification, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"25247294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CHD5 is a chromatin remodeling ATPase that exposes nucleosomal DNA at discrete positions (nucleosome unwrapping) in an ATP hydrolysis-dependent manner; continued ATP hydrolysis is not required to maintain the remodeled state, and this activity is distinct from ACF and BRG1, which reposition nucleosomes. CHD4 shows strong ATPase activity but does not unwrap nucleosomes as efficiently as CHD5.\",\n      \"method\": \"In vitro nucleosome remodeling assay, ATPase assay, comparison with related remodeling ATPases\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical reconstitution of enzymatic activity with mechanistic dissection, single lab\",\n      \"pmids\": [\"24923445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Chd5 orchestrates a cascade of molecular events during spermiogenesis required for histone removal and replacement: H4 hyperacetylation, histone variant expression, nucleosome eviction, DNA damage repair, and expression of transition proteins (Tnp1/Tnp2) and protamines (Prm1/2). Chd5 deficiency leads to defective sperm chromatin compaction and male infertility.\",\n      \"method\": \"Chd5 knockout mouse, spermiogenesis phenotyping, molecular analysis of histone modifications, gene expression (mRNA), chromatin compaction assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with multiple orthogonal molecular readouts, replicates and extends findings from PMID:24252660\",\n      \"pmids\": [\"24818823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CHD5 is expressed during neuronal differentiation in the developing mouse brain; Chd5 subcellular localization switches from cytoplasm to nucleus during mid-gestation, and high nuclear levels are maintained in differentiated adult neurons.\",\n      \"method\": \"Immunostaining of endogenous Chd5 protein across developmental time points in mouse brain sections, subcellular localization analysis\",\n      \"journal\": \"Gene expression patterns : GEP\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment across multiple developmental stages, single lab, no functional manipulation linked to localization switch\",\n      \"pmids\": [\"24120991\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CHD5 is a nucleosome-stimulated ATPase (demonstrated with recombinant zebrafish Chd5 protein in vitro); knockdown of Chd5 during zebrafish embryogenesis causes craniofacial development defects and impaired dopaminergic amacrine cell differentiation, establishing a conserved role in neuronal differentiation.\",\n      \"method\": \"In vitro nucleosome remodeling/ATPase assay with recombinant protein, morpholino knockdown in zebrafish, neural marker expression analysis\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro ATPase assay plus in vivo KD phenotype, single lab, zebrafish ortholog\",\n      \"pmids\": [\"26092436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CHD5 is clearly associated with all canonical NuRD components—MTA1/2, GATAD2A, HDAC1/2, RBBP4/7, and MBD2/3—as determined by immunoprecipitation from neuroblastoma cell nuclear extracts and confirmed by MS/MS analysis. GST-FOG1 pulldown also identified NuRD components associated with CHD5.\",\n      \"method\": \"Co-immunoprecipitation from endogenous and V5-tagged CHD5 cells, GST-FOG1 pulldown, MS/MS mass spectrometry, Western blotting\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus GST pulldown plus MS/MS confirmation, multiple orthogonal methods in a single focused study\",\n      \"pmids\": [\"25825869\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Chd5 represses murine endogenous retrovirus-L (MuERV-L/MERVL) retrotransposons in mouse embryonic stem cells by regulating H3K27me3 modification and histone H3.1/H3.2 incorporation.\",\n      \"method\": \"CRISPR-Cas9 knockout of Chd5 locus in mESCs, analysis of MERVL expression, ChIP for H3K27me3, histone variant analysis\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean CRISPR KO with molecular readouts for specific chromatin modifications and retrotransposon expression, single lab\",\n      \"pmids\": [\"26359639\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CHD5 expression in spermatogenesis is restricted to post-meiotic round spermatids with a maximum at stage VIII, shows complementary expression with CHD3/4, and CHD5 co-localizes with macroH2A1.2 at centromeres and part of the Y chromosome in post-meiotic cells, suggesting a role in sex chromosome chromatin regulation. CHD5 was demonstrated to be a nucleosome-stimulated ATPase in vitro.\",\n      \"method\": \"Immunostaining of mouse testis sections across spermatogenic stages, co-localization with macroH2A1.2, in vitro ATPase assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiments with functional ATPase assay, single lab, two orthogonal methods\",\n      \"pmids\": [\"24849318\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The lysine demethylase JMJD2A/KDM4A transcriptionally represses CHD5, blocking Ras-induced upregulation of CHD5 and thereby reducing p53 pathway activity to promote cellular transformation.\",\n      \"method\": \"Gene expression analysis after JMJD2A overexpression/depletion, oncogenic Ras cooperation assays, cellular senescence assays, p53 pathway reporter assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — CHD5 identified as a transcriptional target of JMJD2A with functional pathway consequence, single lab, limited direct mechanistic detail on CHD5 itself\",\n      \"pmids\": [\"23168260\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"miR-211 directly binds the 3'-UTR of CHD5 mRNA, causing ~50% reduction in CHD5 protein level and promoting colorectal cancer cell proliferation, migration, and tumor growth; enforced miR-211 expression alters p53 pathway proteins (MDM2, Bcl-2, Bcl-xL, Bax).\",\n      \"method\": \"Lentiviral miR-211 overexpression, luciferase 3'-UTR reporter assay, Western blot, xenograft tumor assay, flow cytometry\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — 3'-UTR luciferase assay confirming direct miRNA-mRNA interaction, functional assays in vitro and in vivo, single lab\",\n      \"pmids\": [\"22235338\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CHD5 acts as a transcriptional repressor of multiple oncogenes (MYC, MDM2, STAT3, CCND1, YAP1), epigenetic master genes (Bmi-1, EZH2, JMJD2C), and EMT/stem cell markers (SNAI1, FN1, OCT4) in renal cell carcinoma cells; ChIP assays confirmed direct CHD5 binding to target gene promoters.\",\n      \"method\": \"Ectopic CHD5 expression in RCC cells, qRT-PCR, Western blot, chromatin immunoprecipitation (ChIP), clonogenicity/migration/invasion assays\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP confirming direct promoter binding plus functional gene expression changes, single lab\",\n      \"pmids\": [\"26943038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CHD5 and EZH2 mutually repress each other's transcription: CHD5 is epigenetically silenced by PRC2-mediated H3K27me3 in HCC cells, and overexpression of CHD5 in turn represses EZH2 and activates PRC2 target genes p16 and p21. ChIP and luciferase reporter assays confirmed reciprocal promoter binding.\",\n      \"method\": \"ChIP for H3K27me3, ChIP for CHD5 and EZH2 binding to respective promoters, luciferase reporter assays, gain-of-function CHD5 expression\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and luciferase reporter assays with multiple orthogonal approaches, single lab\",\n      \"pmids\": [\"26517514\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CHD5 upregulation is induced by retinoic acid (13cRA) treatment in a time- and dose-dependent manner only in neuroblastoma cell lines that subsequently undergo neuronal differentiation; NGF/TrkA signaling also induces CHD5 upregulation and differentiation, placing CHD5 downstream of TrkA signaling.\",\n      \"method\": \"13cRA treatment of NB cell lines, qRT-PCR, Western blot, pan-TRK inhibitor blockade, TrkA transfection experiments, morphological differentiation assessment\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — genetic pathway placement by pharmacological inhibition and receptor expression experiments, single lab, multiple cell lines\",\n      \"pmids\": [\"26245651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CHD5 forced expression in neuroblastoma cells with 1p loss inhibits anchorage-independent growth, migration, and invasion in vitro, and delays/reduces bone marrow and liver metastasis in vivo. Genome-wide mRNA sequencing revealed upregulation of the metastasis suppressor PLCL1; knockdown of PLCL1 or p53 reversed CHD5-induced inhibition of invasion, placing PLCL1 and p53 as downstream effectors of CHD5 metastasis suppression.\",\n      \"method\": \"Forced CHD5 expression in NB cell lines, in vitro migration/invasion/anchorage-independent growth assays, intravenous xenograft mouse model, genome-wide RNA-seq, PLCL1 and p53 knockdown epistasis experiments\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis experiments with RNA-seq and in vivo validation, single lab\",\n      \"pmids\": [\"34789839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Chd5 promotes neuronal differentiation by directing stepwise transcriptional changes: during early neurogenesis, Chd5 promotes expression of the proneural transcription factor Six3, which in turn represses Wnt5a (a non-canonical Wnt ligand required for neuronal maturation), establishing a Chd5→Six3→Wnt5a regulatory axis critical for lineage specification.\",\n      \"method\": \"Transcriptional profiling of Chd5-deficient mouse cells at early and late neuronal differentiation stages, genetic epistasis using Chd5 knockout mouse model\",\n      \"journal\": \"Stem cells (Dayton, Ohio)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO model with transcriptional profiling establishing pathway hierarchy, single lab\",\n      \"pmids\": [\"36636025\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"CHD5 promoter CpG island hypermethylation silences CHD5 expression in cancer; CHD5 is the only CHD family member (CHD1-9) whose promoter is hypermethylated in human cancer cell lines and primary tumors (gliomas, colon, breast carcinomas). Treatment with DNA demethylating agent restores CHD5 mRNA expression.\",\n      \"method\": \"Methylation profiling of CHD family members in cancer lines and primary tumors, RT-qPCR, 5-aza-2'-deoxycytidine demethylation treatment\",\n      \"journal\": \"Epigenetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — systematic comparison across all CHD family members with functional demethylation rescue, single lab\",\n      \"pmids\": [\"18698156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The transcription factor AP2 activates CHD5 promoter activity; CHD5 promoter methylation represses AP2 recruitment and reduces promoter activity. Treatment with DNA methyltransferase inhibitor DAC increases AP2 recruitment to the CHD5 promoter.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP-PCR), luciferase reporter assay, AP2 overexpression, DAC treatment\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, ChIP and reporter assay only, limited mechanistic dissection\",\n      \"pmids\": [\"24454811\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CHD5 is an ATP-dependent chromatin remodeling ATPase that assembles into a NuRD-type repressor complex (with HDAC1/2, MTA1/2, GATAD2A, RBBP4/7, MBD2/3), binds the unmodified N-terminus of histone H3 via its tandem PHD fingers, remodels nucleosomes by DNA unwrapping, and functions as a tumor suppressor by transcriptionally repressing target genes (including WEE1 and oncogenes) and activating p19Arf/p53 pathway-dependent proliferation control, apoptosis, and senescence; in the germline it orchestrates the histone-to-protamine chromatin remodeling cascade essential for spermiogenesis, and in the developing brain it promotes neuronal differentiation through a Chd5→Six3→Wnt5a transcriptional axis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CHD5 is an ATP-dependent chromatin-remodeling ATPase that functions as a tumor suppressor and a master regulator of cell-fate transitions in the nervous system and germline [#0, #3]. Biochemically, CHD5 is a nucleosome-stimulated ATPase that remodels nucleosomes by exposing nucleosomal DNA (unwrapping) in an ATP-hydrolysis-dependent manner, an activity distinct from the nucleosome-repositioning enzymes ACF and BRG1 and more efficient at unwrapping than its paralog CHD4 [#6, #12]. Its tandem PHD fingers read the unmodified N-terminus of histone H3, engaging two H3 tails simultaneously with enhanced affinity, while modifications at H3R2, H3K4, H3T3, H3T6, and H3S10 abolish binding [#2]. CHD5 assembles into a megadalton NuRD-type repressor complex containing HDAC1/2, MTA1/2, GATAD2A, RBBP4/7, and MBD2/3, and its incorporation appears mutually exclusive with CHD4 [#1, #10, #5]. Chromatin engagement is essential for function: PHD mutations that abolish H3 binding eliminate CHD5's ability to inhibit proliferation, modulate target genes, and suppress tumors, and a catalytically inactive mutant still joins NuRD but fails to repress transcription [#3, #5]. Through direct promoter binding, CHD5 represses the G2/M regulator WEE1 and a broad oncogenic program (MYC, MDM2, STAT3, CCND1, YAP1, EZH2, Bmi-1) while controlling proliferation, apoptosis, and senescence via the p19Arf/p53 pathway [#5, #15, #0]; its tumor-suppressor output extends to metastasis through a CHD5\\u2192PLCL1/p53 axis [#18]. In the developing brain CHD5 drives neuronal differentiation, in part via a Chd5\\u2192Six3\\u2192Wnt5a transcriptional cascade [#19], and in the male germline it orchestrates the histone-to-protamine transition required for sperm chromatin condensation [#4, #7]. CHD5 is itself silenced in cancer by promoter CpG hypermethylation, PRC2-mediated H3K27me3, and post-transcriptional repression by miR-211 [#20, #16, #14].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established CHD5 as a genuine tumor suppressor acting through a defined pathway, answering whether the 1p36 candidate gene had causal anti-tumor activity in vivo.\",\n      \"evidence\": \"Chromosome engineering of mouse gain/loss models with p19Arf/p53 pathway epistasis\",\n      \"pmids\": [\"17289567\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the molecular/enzymatic activity of CHD5\", \"Direct gene targets not yet identified\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Explained how CHD5 is inactivated in human tumors without mutation, showing promoter CpG hypermethylation uniquely silences CHD5 among CHD family members.\",\n      \"evidence\": \"Methylation profiling of CHD1-9 in cancer lines/primary tumors with 5-aza demethylation rescue\",\n      \"pmids\": [\"18698156\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Correlative across tumor types\", \"Did not address downstream consequences of silencing on specific targets\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Provided the first biochemical picture of CHD5 as a NuRD-like complex member that binds neuronal gene promoters, linking it to transcriptional repression in neurons.\",\n      \"evidence\": \"Co-IP, ChIP, expression profiling and fractionation from mouse brain\",\n      \"pmids\": [\"21931736\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Partial complex composition only\", \"No catalytic or remodeling mechanism defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined the histone reader specificity of CHD5, showing tandem PHD fingers recognize unmodified H3 N-termini and engage two tails cooperatively.\",\n      \"evidence\": \"Peptide arrays, NMR, SPR and quantitative binding assays\",\n      \"pmids\": [\"22834704\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vitro peptide system, not nucleosomal context\", \"Did not link binding to in vivo function\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified upstream regulators of CHD5, placing it under control of JMJD2A/KDM4A and miR-211 to connect CHD5 loss to the p53 pathway and tumor growth.\",\n      \"evidence\": \"JMJD2A gain/loss with Ras cooperation assays; miR-211 3'-UTR luciferase reporter and xenograft assays\",\n      \"pmids\": [\"23168260\", \"22235338\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Regulatory effects on CHD5 are indirect/post-transcriptional\", \"p53 pathway effects inferred from downstream proteins\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Proved that chromatin binding is mechanistically required for tumor suppression by linking PHD-mediated H3 reading to all functional outputs.\",\n      \"evidence\": \"PHD mutagenesis, genome-wide ChIP-seq, xenograft and neuroblastoma differentiation assays\",\n      \"pmids\": [\"23318260\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the remodeling enzymology\", \"Full target gene network only partially defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Began to dissect transcriptional control of CHD5 itself, showing AP2 activates the CHD5 promoter in a methylation-sensitive manner.\",\n      \"evidence\": \"ChIP-PCR, luciferase reporter, AP2 overexpression, DAC treatment\",\n      \"pmids\": [\"24454811\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Limited mechanistic dissection, ChIP and reporter only\", \"No in vivo validation\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the enzymatic mechanism, defining CHD5 as a nucleosome-stimulated ATPase that unwraps rather than repositions nucleosomes, distinguishing it from ACF, BRG1, and CHD4.\",\n      \"evidence\": \"In vitro nucleosome remodeling and ATPase assays with comparison to related ATPases; recombinant zebrafish protein assays\",\n      \"pmids\": [\"24923445\", \"26092436\", \"24849318\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of unwrapping not determined\", \"Physiological consequences of unwrapping vs repositioning unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Completed the NuRD complex membership map and tied catalytic activity to repression, showing CHD5/NuRD represses WEE1 and that catalytic activity (not complex assembly) is required for repression.\",\n      \"evidence\": \"Endogenous complex purification, reciprocal Co-IP, GST-FOG1 pulldown, MS/MS, catalytically inactive mutant analysis\",\n      \"pmids\": [\"25247294\", \"25825869\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of CHD5/CHD4 mutual exclusivity unresolved\", \"Full target gene repertoire not exhaustively defined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Established a germline function, showing CHD5 is required for the histone-to-protamine transition and sperm chromatin condensation.\",\n      \"evidence\": \"Chd5 knockout mice with histology, EM, histone-modification immunofluorescence and gene expression of transition proteins/protamines\",\n      \"pmids\": [\"24252660\", \"24818823\", \"24849318\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct chromatin targets in spermatids not mapped\", \"Mechanistic link from H4 hyperacetylation to nucleosome eviction incomplete\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connected CHD5 expression to neuronal differentiation programs and placed it downstream of retinoic acid and NGF/TrkA signaling.\",\n      \"evidence\": \"Developmental immunostaining in mouse brain; 13cRA and TrkA induction with pan-TRK blockade in neuroblastoma lines\",\n      \"pmids\": [\"24120991\", \"26245651\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cause of cytoplasm-to-nucleus localization switch unknown\", \"Mechanism linking TrkA signaling to CHD5 induction undefined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Broadened CHD5's repressive target spectrum and revealed reciprocal antagonism with PRC2/EZH2 and silencing by H3K27me3.\",\n      \"evidence\": \"ChIP, luciferase reporters and gain-of-function expression in RCC and HCC cells; CRISPR KO mESC analysis of MERVL/H3K27me3\",\n      \"pmids\": [\"26943038\", \"26517514\", \"26359639\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lineage observations not generalized\", \"Direct vs indirect repression of each target not fully separated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended tumor suppression beyond proliferation to metastasis, identifying a CHD5\\u2192PLCL1/p53 effector axis.\",\n      \"evidence\": \"Forced expression in neuroblastoma, RNA-seq, in vivo metastasis model, PLCL1/p53 knockdown epistasis\",\n      \"pmids\": [\"34789839\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PLCL1 is a direct CHD5 target not established\", \"Mechanism of p53 cooperation in metastasis unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined a transcriptional hierarchy for CHD5 in neurogenesis, establishing the Chd5\\u2192Six3\\u2192Wnt5a axis for neuronal lineage specification.\",\n      \"evidence\": \"Transcriptional profiling and genetic epistasis in Chd5 knockout mouse cells across differentiation stages\",\n      \"pmids\": [\"36636025\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether Six3 is a direct chromatin target of CHD5 not shown\", \"NuRD requirement for this axis not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CHD5's nucleosome-unwrapping activity, PHD-mediated H3 reading, and NuRD assembly are integrated into target-gene selection across distinct tissues remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of CHD5 on a nucleosome\", \"Determinants of tissue-specific target selection unknown\", \"Basis for CHD5 vs CHD4 NuRD partitioning unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [6, 9, 12]},\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [5, 15, 16]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [6, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 8]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2, 6, 11]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [5, 15, 19]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 18, 20]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [9, 19]}\n    ],\n    \"complexes\": [\"NuRD complex\"],\n    \"partners\": [\"HDAC1\", \"HDAC2\", \"MTA1\", \"MTA2\", \"GATAD2A\", \"RBBP4\", \"MBD2\", \"MBD3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":8,"faith_total":8,"faith_pct":100.0}}