{"gene":"TG_209910","gene_symbol":"","run_date":"2026-09-08T11:06:21","timeline":{"discoveries":[{"year":2009,"finding":"A novel H2B variant (H2Bv) interacts with H2AZ and H2A1 but not with H2AX, revealing a selective nucleosome composition in Toxoplasma gondii.","method":"Protein interaction assay (pulldown/Co-IP implied by interaction characterization)","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, interaction specificity shown for multiple H2A partners, but abstract does not detail method rigor (no reciprocal Co-IP or reconstitution explicitly described)","pmids":["19607843"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2009,"finding":"Chromatin immunoprecipitation (ChIP) revealed that H2Bv is enriched at actively transcribed genes, indicating a role for H2Bv-containing nucleosomes in marking transcriptionally active chromatin.","method":"Chromatin immunoprecipitation (ChIP)","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP is a direct localization method with functional implication; single lab but uses a well-established technique with a clear functional readout","pmids":["19607843"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii H2Bv is a non-canonical histone H2B variant that selectively interacts with H2AZ and H2A1 (but not H2AX) to form novel nucleosome compositions, and is enriched at actively transcribed genes as determined by ChIP, suggesting it marks transcriptionally permissive chromatin in this parasite."},"narrative":{"mechanistic_narrative":"Toxoplasma gondii H2Bv is a non-canonical histone H2B variant that defines specialized nucleosome compositions in this parasite by selectively pairing with a restricted set of H2A partners: it interacts with H2AZ and H2A1 but not with H2AX [PMID:19607843]. Chromatin immunoprecipitation places H2Bv-containing nucleosomes preferentially at actively transcribed genes, marking transcriptionally permissive chromatin [PMID:19607843]. Beyond this selective partner association and its enrichment at active loci, no further mechanistic detail — including how H2Bv deposition is targeted or how it influences transcription — has been characterized in the available corpus.","teleology":[{"year":2009,"claim":"Whether Toxoplasma encodes a distinct H2B variant with a defined nucleosome partner selectivity was unknown; identifying its selective interaction with H2AZ and H2A1 but not H2AX established that H2Bv builds specific, non-random nucleosome compositions.","evidence":"Protein interaction assay characterizing H2Bv associations with multiple H2A partners in T. gondii","pmids":["19607843"],"confidence":"Medium","gaps":["No reciprocal Co-IP or in vitro reconstitution reported to confirm direct pairing","Stoichiometry and structure of the H2Bv-H2AZ/H2A1 nucleosome not defined","Mechanism excluding H2AX from H2Bv nucleosomes unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2009,"claim":"Whether H2Bv-containing nucleosomes have a genomic distribution linked to transcription was unresolved; ChIP enrichment at actively transcribed genes established that H2Bv marks transcriptionally permissive chromatin.","evidence":"Chromatin immunoprecipitation of H2Bv across T. gondii genes","pmids":["19607843"],"confidence":"Medium","gaps":["Causality between H2Bv presence and active transcription not tested (correlation only)","Deposition/eviction machinery targeting H2Bv to active genes unidentified","No knockdown/knockout phenotype linking H2Bv to gene expression"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"How H2Bv is deposited, what factors direct it to active genes, and whether it is functionally required for transcription in Toxoplasma remain unknown.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No chaperone or remodeler identified for H2Bv deposition","No loss-of-function phenotype established","No structural model of H2Bv nucleosomes"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["H2Bv-H2AZ nucleosome","H2Bv-H2A1 nucleosome"],"partners":["H2AZ","H2A1"],"other_free_text":["H2Bv does not interact with H2AX, defining a selective H2A partner spectrum [#0]","H2Bv is enriched at actively transcribed genes by ChIP, marking transcriptionally permissive chromatin [#1]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"19607843","id":"PMC_19607843","title":"Toxoplasma H2A variants reveal novel insights into nucleosome composition and functions for this histone family.","date":"2009","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19607843","citation_count":51,"is_preprint":false},{"pmid":"23199404","id":"PMC_23199404","title":"Toxoplasma histone acetylation remodelers as novel drug targets.","date":"2012","source":"Expert review of anti-infective therapy","url":"https://pubmed.ncbi.nlm.nih.gov/23199404","citation_count":47,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3426,"output_tokens":537,"usd":0.009166,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5219,"output_tokens":1516,"usd":0.031997,"stage2_stop_reason":"end_turn"},"total_usd":0.041163,"stage1_batch_id":"msgbatch_01WokvBYTB6JLnYrpD4rXnyV","stage2_batch_id":"msgbatch_01M7hsQDvz6AqVC9DLVjQzzc","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2009,\n      \"finding\": \"A novel H2B variant (H2Bv) interacts with H2AZ and H2A1 but not with H2AX, revealing a selective nucleosome composition in Toxoplasma gondii.\",\n      \"method\": \"Protein interaction assay (pulldown/Co-IP implied by interaction characterization)\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, interaction specificity shown for multiple H2A partners, but abstract does not detail method rigor (no reciprocal Co-IP or reconstitution explicitly described)\",\n      \"pmids\": [\"19607843\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Chromatin immunoprecipitation (ChIP) revealed that H2Bv is enriched at actively transcribed genes, indicating a role for H2Bv-containing nucleosomes in marking transcriptionally active chromatin.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP)\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP is a direct localization method with functional implication; single lab but uses a well-established technique with a clear functional readout\",\n      \"pmids\": [\"19607843\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii H2Bv is a non-canonical histone H2B variant that selectively interacts with H2AZ and H2A1 (but not H2AX) to form novel nucleosome compositions, and is enriched at actively transcribed genes as determined by ChIP, suggesting it marks transcriptionally permissive chromatin in this parasite.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"Toxoplasma gondii H2Bv is a non-canonical histone H2B variant that defines specialized nucleosome compositions in this parasite by selectively pairing with a restricted set of H2A partners: it interacts with H2AZ and H2A1 but not with H2AX [#0]. Chromatin immunoprecipitation places H2Bv-containing nucleosomes preferentially at actively transcribed genes, marking transcriptionally permissive chromatin [#1]. Beyond this selective partner association and its enrichment at active loci, no further mechanistic detail — including how H2Bv deposition is targeted or how it influences transcription — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Whether Toxoplasma encodes a distinct H2B variant with a defined nucleosome partner selectivity was unknown; identifying its selective interaction with H2AZ and H2A1 but not H2AX established that H2Bv builds specific, non-random nucleosome compositions.\",\n      \"evidence\": \"Protein interaction assay characterizing H2Bv associations with multiple H2A partners in T. gondii\",\n      \"pmids\": [\"19607843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No reciprocal Co-IP or in vitro reconstitution reported to confirm direct pairing\",\n        \"Stoichiometry and structure of the H2Bv-H2AZ/H2A1 nucleosome not defined\",\n        \"Mechanism excluding H2AX from H2Bv nucleosomes unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Whether H2Bv-containing nucleosomes have a genomic distribution linked to transcription was unresolved; ChIP enrichment at actively transcribed genes established that H2Bv marks transcriptionally permissive chromatin.\",\n      \"evidence\": \"Chromatin immunoprecipitation of H2Bv across T. gondii genes\",\n      \"pmids\": [\"19607843\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Causality between H2Bv presence and active transcription not tested (correlation only)\",\n        \"Deposition/eviction machinery targeting H2Bv to active genes unidentified\",\n        \"No knockdown/knockout phenotype linking H2Bv to gene expression\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How H2Bv is deposited, what factors direct it to active genes, and whether it is functionally required for transcription in Toxoplasma remain unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No chaperone or remodeler identified for H2Bv deposition\",\n        \"No loss-of-function phenotype established\",\n        \"No structural model of H2Bv nucleosomes\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0046982\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000786\", \"supporting_discovery_ids\": [0, 1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006355\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"H2Bv-H2AZ nucleosome\", \"H2Bv-H2A1 nucleosome\"],\n    \"partners\": [\"H2AZ\", \"H2A1\"],\n    \"other_free_text\": [\n      \"H2Bv does not interact with H2AX, defining a selective H2A partner spectrum [#0]\",\n      \"H2Bv is enriched at actively transcribed genes by ChIP, marking transcriptionally permissive chromatin [#1]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_209910","name":null,"product":"histone H2Bv","uniprot_acc":"A0A125YMF5","chromosome":"TGME49_chrIb","start_pos":1546015},{"strain":"GT1","gene_id":"TGGT1_209910","name":null,"product":"histone H2Bv","uniprot_acc":null,"chromosome":"TGGT1_chrIb","start_pos":1562803},{"strain":"RH88","gene_id":"TGRH88_021270","name":null,"product":"histone H2Bv","uniprot_acc":null,"chromosome":"CM023082","start_pos":464360},{"strain":"VEG","gene_id":"TGVEG_209910","name":null,"product":"histone H2Bv","uniprot_acc":"A0A0F7UNS9","chromosome":"TGVEG_chrIb","start_pos":1550896}]}