{"gene":"CDYL2","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2008,"finding":"The CDYL2 chromodomain binds with comparable strength to multiple lysine-methylated ARK(S/T) motifs (including H3K9me3 and related marks), in contrast to CDY which shows discriminatory binding; full-length CDYL2 shows corresponding variability in chromatin localization. Point mutations in the CDYL chromodomain can rescue binding to these motifs.","method":"In vitro methyllysine binding assays, in vivo chromatin localization experiments, point mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro binding assays combined with mutagenesis and in vivo chromatin localization, replicated across multiple ARK(S/T) motifs in a single rigorous study","pmids":["18450745"],"is_preprint":false},{"year":2020,"finding":"Crystal/structural analysis revealed that CDYL2 chromodomain preferentially binds H3tK27me3 over H3K27me3, providing a structural basis for its binding selectivity distinct from CDY1 (which selectively binds H3K9me3). The CDYL1/2-selective compound UNC4850 provided further mechanistic insight into CDYL2 binding specificity.","method":"Crystal structure determination, structural analysis, compound binding studies","journal":"Cell chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional validation using selective chemical probe, single study with multiple orthogonal methods","pmids":["32470319"],"is_preprint":false},{"year":2020,"finding":"CDYL2 co-immunoprecipitates with G9a/EHMT2 and GLP/EHMT1, and regulates chromatin enrichment of G9a and EZH2 at MIR124 gene loci, resulting in epigenetic repression of MIR124 and downstream activation of NF-κB and STAT3 signaling, promoting breast cancer cell plasticity, migration, invasion, and EMT.","method":"Co-immunoprecipitation, ChIP-qPCR, RNAi knockdown with functional assays (migration, invasion, EMT markers)","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus ChIP with functional phenotypic rescue, single lab with two orthogonal methods","pmids":["32450513"],"is_preprint":false},{"year":2020,"finding":"CDYL2 generates four transcript variants (CDYL2a–CDYL2d). CDYL2a localizes to SC35-positive nuclear speckles and promotes alternative splicing (exon skipping) of target genes FIP1L1, NKTR, and ADD3, promoting cell proliferation. CDYL2b localizes to heterochromatin and transcriptionally represses metastasis-promoting genes HPSE, HLA-F, and SELL, suppressing breast cancer cell migration and invasion.","method":"Immunofluorescent staining, RNA-seq, ATAC-seq, ChIP-qPCR, RNAi knockdown with rescue experiments, in vitro and in vivo functional assays","journal":"Theranostics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (localization, transcriptomics, chromatin accessibility, ChIP) plus rescue experiments establishing isoform-specific mechanisms","pmids":["32373210"],"is_preprint":false},{"year":2022,"finding":"CDYL2 down-regulates SLC7A6 expression by decreasing H3K4me3 enrichment at the SLC7A6 promoter, thereby suppressing amino acid transport and inhibiting the mTORC1/S6K pathway. STAT5A was identified as a direct positive transcriptional regulator of CDYL2.","method":"ChIP-qPCR (H3K4me3 at SLC7A6 promoter), gain- and loss-of-function experiments, in vitro and in vivo functional assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP combined with gain/loss-of-function experiments and pathway readout (mTORC1/S6K), single lab","pmids":["35314791"],"is_preprint":false},{"year":2023,"finding":"CDYL2 is recruited to pericentromeres in an H3K9me3-dependent manner, where it interacts (via a central non-conserved region) with mitotic regulators CHAMP1 and POGZ, identified by mass spectrometry. Both the CDYL2 chromodomain and the CHAMP1-POGZ interacting region are required and together sufficient for CDYL2's role in mitotic fidelity and genome stability. CDYL2 RNAi caused loss of CHAMP1 at pericentromeres, nuclear aberrations, and mitotic errors.","method":"Mass spectrometry of CDYL2-interacting proteins, RNAi knockdown, RNAi rescue assays with domain mutants, immunofluorescence (pericentromere localization, CHAMP1 localization)","journal":"Cellular and molecular life sciences : CMLS","confidence":"High","confidence_rationale":"Tier 2 / Strong — MS-identified interaction partners validated by RNAi rescue with domain mapping and multiple functional readouts in a single rigorous study","pmids":["36658409"],"is_preprint":false},{"year":2011,"finding":"Knockdown of Cdyl2 in mouse embryonic stem cells leads to only modest proviral reactivation of ERVs (class I and II), indicating that Cdyl2 is largely dispensable for SETDB1/H3K9me3-dependent retroviral silencing.","method":"shRNA knockdown of Cdyl2 in mESCs with ERV reporter constructs; retroviral reactivation assay","journal":"Epigenetics & chromatin","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct knockdown with specific reporter readout; result is a modest/negative finding but experimentally established","pmids":["21774827"],"is_preprint":false},{"year":2016,"finding":"The PRC1 chemical probe UNC3866 shows submicromolar off-target affinity toward CDYL2 and CDYL chromodomains; an optimized analogue UNC4991 maintains submicromolar affinity toward CDYL chromodomains while displaying a distinct selectivity profile. In vitro pull-down experiments from HeLa nuclear lysates confirmed the selectivity of UNC4991 for CDYL proteins.","method":"Biochemical binding assays, combinatorial peptide library screening, in vitro pull-down from HeLa nuclear lysates","journal":"ACS chemical biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding and pull-down with selectivity profiling, single lab, two orthogonal methods","pmids":["27356154"],"is_preprint":false},{"year":2025,"finding":"CDYL2 isoforms can form homo- and heteromers. CDYL2b is tightly associated with chromatin in prostate cancer cells, and overexpression of CDYL2b suppresses prostate cancer cell growth in vitro and tumor expansion in vivo. JMJD2B (but not JMJD2A) forms complexes with CDYL2b and antagonizes CDYL2b in upregulating HES7 transcription. JMJD2A and JMJD2B suppress CDYL2 transcription.","method":"Co-immunoprecipitation (JMJD2B–CDYL2b complex), overexpression and knockdown with in vitro and in vivo functional assays, RNA sequencing, chromatin fractionation","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional assays and RNA-seq, single lab, multiple orthogonal methods","pmids":["40812719"],"is_preprint":false},{"year":2008,"finding":"Bovine CDYL2 (bCDYL2) is expressed ubiquitously across tissues, and in situ hybridization of bovine testis shows bCDYL2 transcripts are found mainly in spermatids, supporting a role in spermatogenesis.","method":"RT-PCR expression analysis, in situ hybridization of bovine testis","journal":"Animal genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization by ISH without functional consequence established, single study","pmids":["18371128"],"is_preprint":false}],"current_model":"CDYL2 is a chromodomain-containing epigenetic reader that recognizes multiple lysine-methylated ARK(S/T) histone motifs (preferentially H3tK27me3 over H3K27me3 via its chromodomain), is recruited to pericentromeric H3K9me3 where it acts as an adaptor connecting this mark to the mitotic regulators CHAMP1 and POGZ to ensure genome stability, interacts with the histone methyltransferases G9a/EHMT2 and GLP/EHMT1 to epigenetically repress target genes (including MIR124 and SLC7A6), and generates functionally distinct isoforms—CDYL2a promotes alternative splicing at nuclear speckles while CDYL2b localizes to heterochromatin to transcriptionally repress metastasis-promoting genes and forms a complex with JMJD2B that antagonizes its transcriptional activity."},"narrative":{"mechanistic_narrative":"CDYL2 is a chromodomain-containing epigenetic reader that couples recognition of methylated histone marks to chromatin-based gene repression and mitotic genome stability [PMID:18450745, PMID:36658409]. Its chromodomain binds multiple lysine-methylated ARK(S/T) motifs with comparatively low selectivity relative to CDY, and structural analysis shows a binding preference for H3tK27me3 over H3K27me3 [PMID:18450745, PMID:32470319]. At pericentromeres, CDYL2 is recruited in an H3K9me3-dependent manner and, through a central non-conserved region, acts as an adaptor linking this mark to the mitotic regulators CHAMP1 and POGZ; both the chromodomain and the CHAMP1-POGZ-interacting region are required and together sufficient for CDYL2's role in mitotic fidelity, and its depletion causes loss of pericentromeric CHAMP1, nuclear aberrations, and mitotic errors [PMID:36658409]. In a transcriptional repression role, CDYL2 co-immunoprecipitates with the histone methyltransferases G9a/EHMT2 and GLP/EHMT1 and modulates chromatin enrichment of G9a and EZH2 to silence MIR124, and it also represses SLC7A6 by reducing promoter H3K4me3, thereby restraining amino acid transport and mTORC1/S6K signaling [PMID:32450513, PMID:35314791]. CDYL2 produces functionally distinct isoforms: CDYL2a localizes to SC35-positive nuclear speckles and promotes exon-skipping alternative splicing of FIP1L1, NKTR, and ADD3, while CDYL2b associates with heterochromatin to repress metastasis-promoting genes (HPSE, HLA-F, SELL) and forms complexes with JMJD2B that antagonize its transcriptional output [PMID:32373210, PMID:40812719].","teleology":[{"year":2008,"claim":"Established the biochemical reader logic of the CDYL2 chromodomain, showing it binds a broad set of methylated ARK(S/T) histone motifs rather than discriminating among them as CDY does, explaining its variable chromatin distribution.","evidence":"In vitro methyllysine binding assays, point mutagenesis, and in vivo chromatin localization","pmids":["18450745"],"confidence":"High","gaps":["Did not define which physiological mark dominates recruitment in vivo","No structural basis for the binding breadth"]},{"year":2020,"claim":"Provided the structural basis for CDYL2 mark selectivity, distinguishing it from CDY1 by preferential recognition of H3tK27me3 over H3K27me3.","evidence":"Crystal structure determination with selective chemical probe (UNC4850) validation","pmids":["32470319"],"confidence":"High","gaps":["Physiological relevance of testis-specific H3tK27me3 binding not established","Does not address H3K9me3-dependent recruitment seen elsewhere"]},{"year":2020,"claim":"Connected CDYL2 to active gene repression by showing it partners with G9a/GLP and controls G9a/EZH2 occupancy at MIR124, linking the reader to a transcriptional silencing program driving breast cancer cell plasticity.","evidence":"Reciprocal Co-IP, ChIP-qPCR, and RNAi with migration/invasion/EMT readouts","pmids":["32450513"],"confidence":"Medium","gaps":["Direct vs indirect recruitment of G9a/EZH2 not resolved","Single-lab functional model"]},{"year":2020,"claim":"Revealed isoform-specific functional partitioning, with CDYL2a driving alternative splicing at nuclear speckles and CDYL2b mediating heterochromatic repression of metastasis genes.","evidence":"Immunofluorescence, RNA-seq, ATAC-seq, ChIP-qPCR, and RNAi-rescue functional assays","pmids":["32373210"],"confidence":"High","gaps":["Mechanism by which CDYL2a influences splicing machinery unknown","Roles of CDYL2c/CDYL2d not characterized"]},{"year":2022,"claim":"Extended CDYL2's repressive reach to metabolic control, showing it lowers SLC7A6 promoter H3K4me3 to suppress amino acid transport and mTORC1/S6K signaling, and identified STAT5A as its upstream transcriptional activator.","evidence":"ChIP-qPCR, gain/loss-of-function, and in vitro/in vivo functional assays","pmids":["35314791"],"confidence":"Medium","gaps":["Mechanism of H3K4me3 reduction (demethylase recruitment) not defined","Single-lab evidence"]},{"year":2023,"claim":"Defined CDYL2 as a pericentromeric adaptor coupling H3K9me3 to the mitotic regulators CHAMP1 and POGZ, establishing a direct role in mitotic fidelity and genome stability.","evidence":"Mass spectrometry of interactors, RNAi rescue with domain mutants, and immunofluorescence of pericentromeric localization","pmids":["36658409"],"confidence":"High","gaps":["How CHAMP1/POGZ enforce mitotic fidelity downstream not detailed","Interaction not structurally resolved"]},{"year":2025,"claim":"Showed CDYL2 isoforms oligomerize and that CDYL2b suppresses prostate cancer growth, with JMJD2B forming a complex that antagonizes CDYL2b-driven HES7 activation, while JMJD2A/B repress CDYL2 transcription.","evidence":"Co-IP, overexpression/knockdown with in vitro/in vivo assays, RNA-seq, and chromatin fractionation","pmids":["40812719"],"confidence":"Medium","gaps":["Stoichiometry and structure of CDYL2b-JMJD2B complex unknown","Direct vs indirect HES7 regulation not resolved"]},{"year":null,"claim":"How CDYL2's distinct activities — pericentromeric mitotic adaptor, HMT-coupled transcriptional repressor, and speckle-associated splicing factor — are coordinated and selected within a cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking isoform choice to function","Endogenous mark-specific recruitment determinants undefined","Physiological role in spermatogenesis suggested only by expression data"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[2,3,4,8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,5]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[3,5]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2,3,4]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[5]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[2,4,8]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[3]}],"complexes":[],"partners":["CHAMP1","POGZ","EHMT2","EHMT1","JMJD2B"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N8U2","full_name":"Chromodomain Y-like protein 2","aliases":[],"length_aa":506,"mass_kda":56.5,"function":"","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8N8U2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CDYL2","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/CDYL2","total_profiled":1310},"omim":[{"mim_id":"618816","title":"CDY-LIKE PROTEIN 2; CDYL2","url":"https://www.omim.org/entry/618816"},{"mim_id":"616264","title":"MAF TRANSCRIPTIONAL REGULATOR RNA, NONCODING; MAFTRR","url":"https://www.omim.org/entry/616264"},{"mim_id":"603778","title":"CDY-LIKE PROTEIN; CDYL","url":"https://www.omim.org/entry/603778"},{"mim_id":"400016","title":"CHROMODOMAIN PROTEIN, Y-LINKED, 1; CDY1","url":"https://www.omim.org/entry/400016"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":13.2}],"url":"https://www.proteinatlas.org/search/CDYL2"},"hgnc":{"alias_symbol":["FLJ38866"],"prev_symbol":[]},"alphafold":{"accession":"Q8N8U2","domains":[{"cath_id":"2.40.50.40","chopping":"10-53","consensus_level":"high","plddt":88.3232,"start":10,"end":53},{"cath_id":"3.90.226.10","chopping":"257-505","consensus_level":"high","plddt":95.4443,"start":257,"end":505}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N8U2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N8U2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N8U2-F1-predicted_aligned_error_v6.png","plddt_mean":71.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CDYL2","jax_strain_url":"https://www.jax.org/strain/search?query=CDYL2"},"sequence":{"accession":"Q8N8U2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N8U2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N8U2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N8U2"}},"corpus_meta":[{"pmid":"18450745","id":"PMC_18450745","title":"Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18450745","citation_count":86,"is_preprint":false},{"pmid":"32552834","id":"PMC_32552834","title":"G9a regulates tumorigenicity and stemness through genome-wide DNA methylation reprogramming in non-small cell lung cancer.","date":"2020","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/32552834","citation_count":39,"is_preprint":false},{"pmid":"27356154","id":"PMC_27356154","title":"Chromodomain Ligand Optimization via Target-Class Directed Combinatorial Repurposing.","date":"2016","source":"ACS chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/27356154","citation_count":39,"is_preprint":false},{"pmid":"21774827","id":"PMC_21774827","title":"H3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral 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Point mutations in the CDYL chromodomain can rescue binding to these motifs.\",\n      \"method\": \"In vitro methyllysine binding assays, in vivo chromatin localization experiments, point mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro binding assays combined with mutagenesis and in vivo chromatin localization, replicated across multiple ARK(S/T) motifs in a single rigorous study\",\n      \"pmids\": [\"18450745\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Crystal/structural analysis revealed that CDYL2 chromodomain preferentially binds H3tK27me3 over H3K27me3, providing a structural basis for its binding selectivity distinct from CDY1 (which selectively binds H3K9me3). The CDYL1/2-selective compound UNC4850 provided further mechanistic insight into CDYL2 binding specificity.\",\n      \"method\": \"Crystal structure determination, structural analysis, compound binding studies\",\n      \"journal\": \"Cell chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional validation using selective chemical probe, single study with multiple orthogonal methods\",\n      \"pmids\": [\"32470319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CDYL2 co-immunoprecipitates with G9a/EHMT2 and GLP/EHMT1, and regulates chromatin enrichment of G9a and EZH2 at MIR124 gene loci, resulting in epigenetic repression of MIR124 and downstream activation of NF-κB and STAT3 signaling, promoting breast cancer cell plasticity, migration, invasion, and EMT.\",\n      \"method\": \"Co-immunoprecipitation, ChIP-qPCR, RNAi knockdown with functional assays (migration, invasion, EMT markers)\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus ChIP with functional phenotypic rescue, single lab with two orthogonal methods\",\n      \"pmids\": [\"32450513\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CDYL2 generates four transcript variants (CDYL2a–CDYL2d). CDYL2a localizes to SC35-positive nuclear speckles and promotes alternative splicing (exon skipping) of target genes FIP1L1, NKTR, and ADD3, promoting cell proliferation. CDYL2b localizes to heterochromatin and transcriptionally represses metastasis-promoting genes HPSE, HLA-F, and SELL, suppressing breast cancer cell migration and invasion.\",\n      \"method\": \"Immunofluorescent staining, RNA-seq, ATAC-seq, ChIP-qPCR, RNAi knockdown with rescue experiments, in vitro and in vivo functional assays\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (localization, transcriptomics, chromatin accessibility, ChIP) plus rescue experiments establishing isoform-specific mechanisms\",\n      \"pmids\": [\"32373210\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CDYL2 down-regulates SLC7A6 expression by decreasing H3K4me3 enrichment at the SLC7A6 promoter, thereby suppressing amino acid transport and inhibiting the mTORC1/S6K pathway. STAT5A was identified as a direct positive transcriptional regulator of CDYL2.\",\n      \"method\": \"ChIP-qPCR (H3K4me3 at SLC7A6 promoter), gain- and loss-of-function experiments, in vitro and in vivo functional assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP combined with gain/loss-of-function experiments and pathway readout (mTORC1/S6K), single lab\",\n      \"pmids\": [\"35314791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CDYL2 is recruited to pericentromeres in an H3K9me3-dependent manner, where it interacts (via a central non-conserved region) with mitotic regulators CHAMP1 and POGZ, identified by mass spectrometry. Both the CDYL2 chromodomain and the CHAMP1-POGZ interacting region are required and together sufficient for CDYL2's role in mitotic fidelity and genome stability. CDYL2 RNAi caused loss of CHAMP1 at pericentromeres, nuclear aberrations, and mitotic errors.\",\n      \"method\": \"Mass spectrometry of CDYL2-interacting proteins, RNAi knockdown, RNAi rescue assays with domain mutants, immunofluorescence (pericentromere localization, CHAMP1 localization)\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — MS-identified interaction partners validated by RNAi rescue with domain mapping and multiple functional readouts in a single rigorous study\",\n      \"pmids\": [\"36658409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Knockdown of Cdyl2 in mouse embryonic stem cells leads to only modest proviral reactivation of ERVs (class I and II), indicating that Cdyl2 is largely dispensable for SETDB1/H3K9me3-dependent retroviral silencing.\",\n      \"method\": \"shRNA knockdown of Cdyl2 in mESCs with ERV reporter constructs; retroviral reactivation assay\",\n      \"journal\": \"Epigenetics & chromatin\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct knockdown with specific reporter readout; result is a modest/negative finding but experimentally established\",\n      \"pmids\": [\"21774827\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The PRC1 chemical probe UNC3866 shows submicromolar off-target affinity toward CDYL2 and CDYL chromodomains; an optimized analogue UNC4991 maintains submicromolar affinity toward CDYL chromodomains while displaying a distinct selectivity profile. In vitro pull-down experiments from HeLa nuclear lysates confirmed the selectivity of UNC4991 for CDYL proteins.\",\n      \"method\": \"Biochemical binding assays, combinatorial peptide library screening, in vitro pull-down from HeLa nuclear lysates\",\n      \"journal\": \"ACS chemical biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding and pull-down with selectivity profiling, single lab, two orthogonal methods\",\n      \"pmids\": [\"27356154\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CDYL2 isoforms can form homo- and heteromers. CDYL2b is tightly associated with chromatin in prostate cancer cells, and overexpression of CDYL2b suppresses prostate cancer cell growth in vitro and tumor expansion in vivo. JMJD2B (but not JMJD2A) forms complexes with CDYL2b and antagonizes CDYL2b in upregulating HES7 transcription. JMJD2A and JMJD2B suppress CDYL2 transcription.\",\n      \"method\": \"Co-immunoprecipitation (JMJD2B–CDYL2b complex), overexpression and knockdown with in vitro and in vivo functional assays, RNA sequencing, chromatin fractionation\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional assays and RNA-seq, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"40812719\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Bovine CDYL2 (bCDYL2) is expressed ubiquitously across tissues, and in situ hybridization of bovine testis shows bCDYL2 transcripts are found mainly in spermatids, supporting a role in spermatogenesis.\",\n      \"method\": \"RT-PCR expression analysis, in situ hybridization of bovine testis\",\n      \"journal\": \"Animal genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization by ISH without functional consequence established, single study\",\n      \"pmids\": [\"18371128\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CDYL2 is a chromodomain-containing epigenetic reader that recognizes multiple lysine-methylated ARK(S/T) histone motifs (preferentially H3tK27me3 over H3K27me3 via its chromodomain), is recruited to pericentromeric H3K9me3 where it acts as an adaptor connecting this mark to the mitotic regulators CHAMP1 and POGZ to ensure genome stability, interacts with the histone methyltransferases G9a/EHMT2 and GLP/EHMT1 to epigenetically repress target genes (including MIR124 and SLC7A6), and generates functionally distinct isoforms—CDYL2a promotes alternative splicing at nuclear speckles while CDYL2b localizes to heterochromatin to transcriptionally repress metastasis-promoting genes and forms a complex with JMJD2B that antagonizes its transcriptional activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CDYL2 is a chromodomain-containing epigenetic reader that couples recognition of methylated histone marks to chromatin-based gene repression and mitotic genome stability [#0, #5]. Its chromodomain binds multiple lysine-methylated ARK(S/T) motifs with comparatively low selectivity relative to CDY, and structural analysis shows a binding preference for H3tK27me3 over H3K27me3 [#0, #1]. At pericentromeres, CDYL2 is recruited in an H3K9me3-dependent manner and, through a central non-conserved region, acts as an adaptor linking this mark to the mitotic regulators CHAMP1 and POGZ; both the chromodomain and the CHAMP1-POGZ-interacting region are required and together sufficient for CDYL2's role in mitotic fidelity, and its depletion causes loss of pericentromeric CHAMP1, nuclear aberrations, and mitotic errors [#5]. In a transcriptional repression role, CDYL2 co-immunoprecipitates with the histone methyltransferases G9a/EHMT2 and GLP/EHMT1 and modulates chromatin enrichment of G9a and EZH2 to silence MIR124, and it also represses SLC7A6 by reducing promoter H3K4me3, thereby restraining amino acid transport and mTORC1/S6K signaling [#2, #4]. CDYL2 produces functionally distinct isoforms: CDYL2a localizes to SC35-positive nuclear speckles and promotes exon-skipping alternative splicing of FIP1L1, NKTR, and ADD3, while CDYL2b associates with heterochromatin to repress metastasis-promoting genes (HPSE, HLA-F, SELL) and forms complexes with JMJD2B that antagonize its transcriptional output [#3, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established the biochemical reader logic of the CDYL2 chromodomain, showing it binds a broad set of methylated ARK(S/T) histone motifs rather than discriminating among them as CDY does, explaining its variable chromatin distribution.\",\n      \"evidence\": \"In vitro methyllysine binding assays, point mutagenesis, and in vivo chromatin localization\",\n      \"pmids\": [\"18450745\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which physiological mark dominates recruitment in vivo\", \"No structural basis for the binding breadth\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Provided the structural basis for CDYL2 mark selectivity, distinguishing it from CDY1 by preferential recognition of H3tK27me3 over H3K27me3.\",\n      \"evidence\": \"Crystal structure determination with selective chemical probe (UNC4850) validation\",\n      \"pmids\": [\"32470319\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological relevance of testis-specific H3tK27me3 binding not established\", \"Does not address H3K9me3-dependent recruitment seen elsewhere\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Connected CDYL2 to active gene repression by showing it partners with G9a/GLP and controls G9a/EZH2 occupancy at MIR124, linking the reader to a transcriptional silencing program driving breast cancer cell plasticity.\",\n      \"evidence\": \"Reciprocal Co-IP, ChIP-qPCR, and RNAi with migration/invasion/EMT readouts\",\n      \"pmids\": [\"32450513\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect recruitment of G9a/EZH2 not resolved\", \"Single-lab functional model\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed isoform-specific functional partitioning, with CDYL2a driving alternative splicing at nuclear speckles and CDYL2b mediating heterochromatic repression of metastasis genes.\",\n      \"evidence\": \"Immunofluorescence, RNA-seq, ATAC-seq, ChIP-qPCR, and RNAi-rescue functional assays\",\n      \"pmids\": [\"32373210\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which CDYL2a influences splicing machinery unknown\", \"Roles of CDYL2c/CDYL2d not characterized\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended CDYL2's repressive reach to metabolic control, showing it lowers SLC7A6 promoter H3K4me3 to suppress amino acid transport and mTORC1/S6K signaling, and identified STAT5A as its upstream transcriptional activator.\",\n      \"evidence\": \"ChIP-qPCR, gain/loss-of-function, and in vitro/in vivo functional assays\",\n      \"pmids\": [\"35314791\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of H3K4me3 reduction (demethylase recruitment) not defined\", \"Single-lab evidence\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined CDYL2 as a pericentromeric adaptor coupling H3K9me3 to the mitotic regulators CHAMP1 and POGZ, establishing a direct role in mitotic fidelity and genome stability.\",\n      \"evidence\": \"Mass spectrometry of interactors, RNAi rescue with domain mutants, and immunofluorescence of pericentromeric localization\",\n      \"pmids\": [\"36658409\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How CHAMP1/POGZ enforce mitotic fidelity downstream not detailed\", \"Interaction not structurally resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed CDYL2 isoforms oligomerize and that CDYL2b suppresses prostate cancer growth, with JMJD2B forming a complex that antagonizes CDYL2b-driven HES7 activation, while JMJD2A/B repress CDYL2 transcription.\",\n      \"evidence\": \"Co-IP, overexpression/knockdown with in vitro/in vivo assays, RNA-seq, and chromatin fractionation\",\n      \"pmids\": [\"40812719\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stoichiometry and structure of CDYL2b-JMJD2B complex unknown\", \"Direct vs indirect HES7 regulation not resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CDYL2's distinct activities — pericentromeric mitotic adaptor, HMT-coupled transcriptional repressor, and speckle-associated splicing factor — are coordinated and selected within a cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking isoform choice to function\", \"Endogenous mark-specific recruitment determinants undefined\", \"Physiological role in spermatogenesis suggested only by expression data\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [2, 3, 4, 8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2, 3, 4]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [2, 4, 8]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CHAMP1\", \"POGZ\", \"EHMT2\", \"EHMT1\", \"JMJD2B\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":5,"faith_pct":100.0}}