{"gene":"TG_239260","gene_symbol":"","run_date":"2026-09-08T12:58:24","timeline":{"discoveries":[{"year":2007,"finding":"Toxoplasma (and Plasmodium) Set8-related proteins catalyze mono-, di-, and trimethylation of histone H4 at lysine 20 (H4K20), in striking contrast to the monomethylase-restricted human Set8. These enzymes are cell cycle regulated and focally enriched at pericentric and telomeric heterochromatin, marking silent heterochromatic domains.","method":"In vitro histone methyltransferase assay, structural analysis of substrate-specific channel residues, immunofluorescence/ChIP localization","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro enzymatic assay combined with structural analysis and mutagenesis of catalytic residues, replicated across two apicomplexan species","pmids":["17562855"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2005,"finding":"TgMYST-A, a MYST family histone acetyltransferase in Toxoplasma gondii, acetylates histone H4 in vitro preferentially at lysines 5, 8, 12, and 16. TgMYST-A localizes to both the nucleus and cytoplasm and is more abundant in tachyzoites than bradyzoites.","method":"In vitro HAT assay with recombinant TgMYST-A; immunofluorescence and subcellular fractionation for localization; Western blot for stage-specific abundance","journal":"Eukaryotic cell","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay with site-specific residue identification, supported by localization and stage-expression data, single lab","pmids":["16339723"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2017,"finding":"Histone H4 lysine 31 (H4K31) within the globular domain undergoes acetylation and monomethylation in Apicomplexa. In Toxoplasma gondii, H4K31 acetylation at promoters correlates with gene expression, while monomethylated H4K31 is enriched in the core body of active genes but inversely correlates with transcription. In P. falciparum, H4K31me1 is enriched at transcriptionally inactive pericentromeric heterochromatin (a region devoid of H3K9me3 and HP1).","method":"ChIP-seq, mass spectrometry to identify modifications, genome-wide correlation with transcription data","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP-seq and mass spectrometry used orthogonally across two apicomplexan species with genome-wide functional correlation","pmids":["29101771"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"Nucleosomes in Toxoplasma subtelomeric-like regions are enriched in histone H4 monomethylated at K20 (H4K20me1) and the histone variant H2A.X, indicating these regions constitute silenced heterochromatin.","method":"ChIP-qPCR with antibodies against H4K20me1 and H2A.X","journal":"BMC genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — ChIP-qPCR is a direct localization method, but single lab, single method, no functional perturbation","pmids":["24417889"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"ME49"}]},{"year":2008,"finding":"Genome-wide ChIP analysis in Toxoplasma gondii shows that acetylated histone H4 (H4ac) marks promoters of actively transcribed genes, co-occurring with H3K4me3 and H3K9ac.","method":"ChIP-chip / chromatin immunoprecipitation coupled to genome-wide analysis","journal":"The Journal of eukaryotic microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genome-wide ChIP data, but review article summarizing other studies; single indirect attribution, no direct functional perturbation reported","pmids":["19120792"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"finding":"HDAC inhibitor Tubastatin A causes a significant increase in nuclear histone H4 acetylation levels in Toxoplasma gondii, impairing endodyogeny and daughter cell budding.","method":"Western blot for H4 acetylation; fluorescence and electron microscopy for morphological phenotype","journal":"International journal for parasitology. Drugs and drug resistance","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — Western blot and morphological microscopy, single lab, pharmacological perturbation without genetic specificity","pmids":["33360687"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":"RH"},{"species":"Toxoplasma gondii","strain":"ME49"}]},{"year":2018,"finding":"Recombinant Toxoplasma gondii histone H4 (rTgH4) binds to murine macrophages, downregulates TLR4 expression, inhibits chemotaxis and proliferation, and promotes phagocytosis, apoptosis, and secretion of nitric oxide, IL-6, TNF-α, IL-10, and IL-1β in vitro.","method":"Immunofluorescence assay for macrophage binding; flow cytometry and ELISA for functional readouts on Ana-1 macrophages incubated with rTgH4","journal":"The Journal of eukaryotic microbiology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method per readout, recombinant protein applied exogenously with no genetic manipulation of parasite","pmids":["29722109"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii histone H4 is subject to multiple post-translational modifications that determine chromatin state and gene regulation: TgMYST-A acetylates H4 at K5/K8/K12/K16 (active marks), H4ac broadly marks active promoters, H4K31ac at promoters correlates with transcription while H4K31me1 in gene bodies inversely correlates with transcription, and H4K20me1 deposited by a Set8-family methyltransferase marks silent pericentromeric and telomeric heterochromatin; additionally, extracellular TgH4 can modulate host macrophage functions in vitro."},"narrative":{"mechanistic_narrative":"Toxoplasma gondii histone H4 is a core chromatin component whose post-translational modification state partitions the genome into active and silent domains [PMID:29101771, PMID:19120792]. The MYST-family acetyltransferase TgMYST-A acetylates H4 in vitro preferentially at lysines 5, 8, 12, and 16 [PMID:16339723], and genome-wide, acetylated H4 (H4ac) marks the promoters of actively transcribed genes alongside H3K4me3 and H3K9ac [PMID:19120792]. A distinct modification within the globular domain, H4K31, is bifunctionally regulated: H4K31 acetylation at promoters correlates with gene expression, whereas H4K31 monomethylation accumulates in the bodies of active genes yet inversely correlates with transcription [PMID:29101771]. Silencing is imposed by methylation of H4K20: a Set8-related methyltransferase catalyzes mono-, di-, and trimethylation of H4K20 and is focally enriched at pericentric and telomeric heterochromatin [PMID:17562855], and H4K20me1 together with the histone variant H2A.X marks subtelomeric-like silenced heterochromatin [PMID:24417889]. Global H4 acetylation levels are functionally coupled to the cell cycle, as HDAC inhibition raises nuclear H4 acetylation and impairs endodyogeny and daughter-cell budding [PMID:33360687]. Beyond its chromatin role, recombinant TgH4 applied exogenously binds murine macrophages and modulates their inflammatory responses in vitro [PMID:29722109].","teleology":[{"year":2005,"claim":"Establishing which enzyme deposits activating H4 acetylation marks in Toxoplasma addressed how the parasite writes active chromatin; identifying TgMYST-A and its target lysines provided the writer for H4 acetylation.","evidence":"In vitro HAT assay with recombinant TgMYST-A plus immunofluorescence and stage-expression analysis","pmids":["16339723"],"confidence":"High","gaps":["Genetic loss-of-function linking TgMYST-A to specific in vivo H4ac sites not established","Functional consequence of individual K5/K8/K12/K16 acetylation not resolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2007,"claim":"Whether apicomplexan parasites can generate higher-order H4K20 methylation states addressed the mechanism of heterochromatin silencing; showing Set8-related enzymes perform mono-, di-, and trimethylation (unlike monomethylase-restricted human Set8) defined the writer for silent-domain marks.","evidence":"In vitro histone methyltransferase assay with structural analysis of substrate channel residues and IF/ChIP localization, across Toxoplasma and Plasmodium","pmids":["17562855"],"confidence":"High","gaps":["Direct genetic requirement of the enzyme for heterochromatin maintenance not tested","Cell-cycle coupling of methylation dynamics not mechanistically dissected"],"attribution":[{"species":"Toxoplasma gondii","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"Mapping where H4 acetylation resides genome-wide addressed whether H4ac correlates with transcription state; finding H4ac at active promoters alongside H3K4me3 and H3K9ac established H4ac as an active-promoter mark.","evidence":"Genome-wide ChIP analysis in Toxoplasma gondii","pmids":["19120792"],"confidence":"Medium","gaps":["Summarized from other studies rather than direct primary perturbation","Causal role of H4ac in transcription not tested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2014,"claim":"Determining the modification landscape of subtelomeric chromatin addressed which marks define silenced domains; enrichment of H4K20me1 and H2A.X identified these regions as heterochromatin.","evidence":"ChIP-qPCR with H4K20me1 and H2A.X antibodies in ME49","pmids":["24417889"],"confidence":"Medium","gaps":["Single method, no functional perturbation","Enzyme responsible for local H4K20me1 not linked in this study"],"attribution":[{"species":"Toxoplasma gondii","strain":"ME49"}]},{"year":2017,"claim":"Whether the globular-domain residue H4K31 carries regulatory information addressed a novel axis of chromatin control; showing H4K31ac marks active promoters while H4K31me1 populates active gene bodies but inversely tracks transcription established a bifunctional, position-dependent mark.","evidence":"ChIP-seq and mass spectrometry with genome-wide transcription correlation across Toxoplasma and Plasmodium","pmids":["29101771"],"confidence":"High","gaps":["Writers/erasers for H4K31 modifications not identified","Mechanism reconciling gene-body H4K31me1 enrichment with transcriptional repression unresolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"Whether TgH4 has a role beyond chromatin addressed a potential host-interaction function; recombinant TgH4 binding and modulating macrophage responses raised an extracellular immunomodulatory activity.","evidence":"IFA binding assay plus flow cytometry and ELISA on Ana-1 macrophages exposed to recombinant TgH4","pmids":["29722109"],"confidence":"Low","gaps":["Recombinant protein applied exogenously with no genetic evidence of native extracellular secretion","Single method per readout, no in vivo confirmation","Receptor mediating macrophage binding not identified"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2020,"claim":"Whether global H4 acetylation is functionally linked to parasite replication addressed the physiological importance of the acetylation balance; HDAC inhibition raising H4ac and blocking endodyogeny connected the mark to cell-cycle progression.","evidence":"Western blot for H4 acetylation and fluorescence/electron microscopy of budding defects after Tubastatin A treatment in RH and ME49","pmids":["33360687"],"confidence":"Medium","gaps":["Pharmacological perturbation lacks genetic specificity for H4 versus other HDAC substrates","Direct causal chain from H4ac to budding machinery not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":"RH"},{"species":"Toxoplasma gondii","strain":"ME49"}]},{"year":null,"claim":"The writers and erasers for H4K31 modifications, the genetic requirement of TgMYST-A and Set8-related methyltransferases for defined H4 marks in vivo, and the mechanistic basis of any native extracellular H4 function remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No enzyme assigned to H4K31 acetylation or monomethylation","No genetic loss-of-function tying specific H4 marks to phenotypes","Native secretion and receptor for extracellular TgH4 unknown"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["TGMYST-A (MYST-FAMILY HISTONE ACETYLTRANSFERASE, ACETYLATES H4 K5/K8/K12/K16)","SET8-RELATED HISTONE METHYLTRANSFERASE (MONO/DI/TRIMETHYLATES H4K20)","HISTONE VARIANT H2A.X (CO-ENRICHED AT SUBTELOMERIC HETEROCHROMATIN)"],"other_free_text":["H4ac and H4K31ac mark active promoters; H4K31me1 marks active gene bodies but inversely correlates with transcription.","H4K20me1/2/3 and H4K20me1 with H2A.X mark silent pericentric, telomeric, and subtelomeric-like heterochromatin.","Global H4 acetylation balance is coupled to endodyogeny; HDAC inhibition (Tubastatin A) raises H4ac and impairs daughter-cell budding.","Recombinant extracellular TgH4 binds murine macrophages and modulates TLR4 expression, chemotaxis, apoptosis, phagocytosis, and cytokine/NO secretion in vitro (Low confidence)."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"17562855","id":"PMC_17562855","title":"SET8-mediated methylations of histone H4 lysine 20 mark silent heterochromatic domains in apicomplexan genomes.","date":"2007","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17562855","citation_count":59,"is_preprint":false},{"pmid":"16339723","id":"PMC_16339723","title":"MYST family histone acetyltransferases in the protozoan parasite Toxoplasma gondii.","date":"2005","source":"Eukaryotic cell","url":"https://pubmed.ncbi.nlm.nih.gov/16339723","citation_count":36,"is_preprint":false},{"pmid":"29101771","id":"PMC_29101771","title":"Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites.","date":"2017","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/29101771","citation_count":34,"is_preprint":false},{"pmid":"33360687","id":"PMC_33360687","title":"HDAC inhibitors Tubastatin A and SAHA affect parasite cell division and are potential anti-Toxoplasma gondii chemotherapeutics.","date":"2020","source":"International journal for parasitology. Drugs and drug resistance","url":"https://pubmed.ncbi.nlm.nih.gov/33360687","citation_count":28,"is_preprint":false},{"pmid":"19379753","id":"PMC_19379753","title":"Transfection of Eimeria and Toxoplasma using heterologous regulatory sequences.","date":"2009","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/19379753","citation_count":17,"is_preprint":false},{"pmid":"19120792","id":"PMC_19120792","title":"How epigenomics contributes to the understanding of gene regulation in Toxoplasma gondii.","date":"2008","source":"The Journal of eukaryotic microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/19120792","citation_count":9,"is_preprint":false},{"pmid":"24417889","id":"PMC_24417889","title":"Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions.","date":"2014","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/24417889","citation_count":9,"is_preprint":false},{"pmid":"29722109","id":"PMC_29722109","title":"Toxoplasma gondii Histone 4 Affects Some Functions of Murine Ana-1 Macrophages In Vitro.","date":"2018","source":"The Journal of eukaryotic microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29722109","citation_count":4,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6443,"output_tokens":2066,"usd":0.02516,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7304,"output_tokens":3738,"usd":0.064985,"stage2_stop_reason":"end_turn"},"total_usd":0.090145,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"Toxoplasma (and Plasmodium) Set8-related proteins catalyze mono-, di-, and trimethylation of histone H4 at lysine 20 (H4K20), in striking contrast to the monomethylase-restricted human Set8. These enzymes are cell cycle regulated and focally enriched at pericentric and telomeric heterochromatin, marking silent heterochromatic domains.\",\n      \"method\": \"In vitro histone methyltransferase assay, structural analysis of substrate-specific channel residues, immunofluorescence/ChIP localization\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro enzymatic assay combined with structural analysis and mutagenesis of catalytic residues, replicated across two apicomplexan species\",\n      \"pmids\": [\"17562855\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"TgMYST-A, a MYST family histone acetyltransferase in Toxoplasma gondii, acetylates histone H4 in vitro preferentially at lysines 5, 8, 12, and 16. TgMYST-A localizes to both the nucleus and cytoplasm and is more abundant in tachyzoites than bradyzoites.\",\n      \"method\": \"In vitro HAT assay with recombinant TgMYST-A; immunofluorescence and subcellular fractionation for localization; Western blot for stage-specific abundance\",\n      \"journal\": \"Eukaryotic cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay with site-specific residue identification, supported by localization and stage-expression data, single lab\",\n      \"pmids\": [\"16339723\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Histone H4 lysine 31 (H4K31) within the globular domain undergoes acetylation and monomethylation in Apicomplexa. In Toxoplasma gondii, H4K31 acetylation at promoters correlates with gene expression, while monomethylated H4K31 is enriched in the core body of active genes but inversely correlates with transcription. In P. falciparum, H4K31me1 is enriched at transcriptionally inactive pericentromeric heterochromatin (a region devoid of H3K9me3 and HP1).\",\n      \"method\": \"ChIP-seq, mass spectrometry to identify modifications, genome-wide correlation with transcription data\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP-seq and mass spectrometry used orthogonally across two apicomplexan species with genome-wide functional correlation\",\n      \"pmids\": [\"29101771\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Nucleosomes in Toxoplasma subtelomeric-like regions are enriched in histone H4 monomethylated at K20 (H4K20me1) and the histone variant H2A.X, indicating these regions constitute silenced heterochromatin.\",\n      \"method\": \"ChIP-qPCR with antibodies against H4K20me1 and H2A.X\",\n      \"journal\": \"BMC genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — ChIP-qPCR is a direct localization method, but single lab, single method, no functional perturbation\",\n      \"pmids\": [\"24417889\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"ME49\"}\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Genome-wide ChIP analysis in Toxoplasma gondii shows that acetylated histone H4 (H4ac) marks promoters of actively transcribed genes, co-occurring with H3K4me3 and H3K9ac.\",\n      \"method\": \"ChIP-chip / chromatin immunoprecipitation coupled to genome-wide analysis\",\n      \"journal\": \"The Journal of eukaryotic microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genome-wide ChIP data, but review article summarizing other studies; single indirect attribution, no direct functional perturbation reported\",\n      \"pmids\": [\"19120792\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"HDAC inhibitor Tubastatin A causes a significant increase in nuclear histone H4 acetylation levels in Toxoplasma gondii, impairing endodyogeny and daughter cell budding.\",\n      \"method\": \"Western blot for H4 acetylation; fluorescence and electron microscopy for morphological phenotype\",\n      \"journal\": \"International journal for parasitology. Drugs and drug resistance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Western blot and morphological microscopy, single lab, pharmacological perturbation without genetic specificity\",\n      \"pmids\": [\"33360687\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"},\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"ME49\"}\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Recombinant Toxoplasma gondii histone H4 (rTgH4) binds to murine macrophages, downregulates TLR4 expression, inhibits chemotaxis and proliferation, and promotes phagocytosis, apoptosis, and secretion of nitric oxide, IL-6, TNF-α, IL-10, and IL-1β in vitro.\",\n      \"method\": \"Immunofluorescence assay for macrophage binding; flow cytometry and ELISA for functional readouts on Ana-1 macrophages incubated with rTgH4\",\n      \"journal\": \"The Journal of eukaryotic microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method per readout, recombinant protein applied exogenously with no genetic manipulation of parasite\",\n      \"pmids\": [\"29722109\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii histone H4 is subject to multiple post-translational modifications that determine chromatin state and gene regulation: TgMYST-A acetylates H4 at K5/K8/K12/K16 (active marks), H4ac broadly marks active promoters, H4K31ac at promoters correlates with transcription while H4K31me1 in gene bodies inversely correlates with transcription, and H4K20me1 deposited by a Set8-family methyltransferase marks silent pericentromeric and telomeric heterochromatin; additionally, extracellular TgH4 can modulate host macrophage functions in vitro.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"Toxoplasma gondii histone H4 is a core chromatin component whose post-translational modification state partitions the genome into active and silent domains [#2, #4]. The MYST-family acetyltransferase TgMYST-A acetylates H4 in vitro preferentially at lysines 5, 8, 12, and 16 [#1], and genome-wide, acetylated H4 (H4ac) marks the promoters of actively transcribed genes alongside H3K4me3 and H3K9ac [#4]. A distinct modification within the globular domain, H4K31, is bifunctionally regulated: H4K31 acetylation at promoters correlates with gene expression, whereas H4K31 monomethylation accumulates in the bodies of active genes yet inversely correlates with transcription [#2]. Silencing is imposed by methylation of H4K20: a Set8-related methyltransferase catalyzes mono-, di-, and trimethylation of H4K20 and is focally enriched at pericentric and telomeric heterochromatin [#0], and H4K20me1 together with the histone variant H2A.X marks subtelomeric-like silenced heterochromatin [#3]. Global H4 acetylation levels are functionally coupled to the cell cycle, as HDAC inhibition raises nuclear H4 acetylation and impairs endodyogeny and daughter-cell budding [#5]. Beyond its chromatin role, recombinant TgH4 applied exogenously binds murine macrophages and modulates their inflammatory responses in vitro [#6].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing which enzyme deposits activating H4 acetylation marks in Toxoplasma addressed how the parasite writes active chromatin; identifying TgMYST-A and its target lysines provided the writer for H4 acetylation.\",\n      \"evidence\": \"In vitro HAT assay with recombinant TgMYST-A plus immunofluorescence and stage-expression analysis\",\n      \"pmids\": [\"16339723\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genetic loss-of-function linking TgMYST-A to specific in vivo H4ac sites not established\", \"Functional consequence of individual K5/K8/K12/K16 acetylation not resolved\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Whether apicomplexan parasites can generate higher-order H4K20 methylation states addressed the mechanism of heterochromatin silencing; showing Set8-related enzymes perform mono-, di-, and trimethylation (unlike monomethylase-restricted human Set8) defined the writer for silent-domain marks.\",\n      \"evidence\": \"In vitro histone methyltransferase assay with structural analysis of substrate channel residues and IF/ChIP localization, across Toxoplasma and Plasmodium\",\n      \"pmids\": [\"17562855\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct genetic requirement of the enzyme for heterochromatin maintenance not tested\", \"Cell-cycle coupling of methylation dynamics not mechanistically dissected\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Mapping where H4 acetylation resides genome-wide addressed whether H4ac correlates with transcription state; finding H4ac at active promoters alongside H3K4me3 and H3K9ac established H4ac as an active-promoter mark.\",\n      \"evidence\": \"Genome-wide ChIP analysis in Toxoplasma gondii\",\n      \"pmids\": [\"19120792\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Summarized from other studies rather than direct primary perturbation\", \"Causal role of H4ac in transcription not tested\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Determining the modification landscape of subtelomeric chromatin addressed which marks define silenced domains; enrichment of H4K20me1 and H2A.X identified these regions as heterochromatin.\",\n      \"evidence\": \"ChIP-qPCR with H4K20me1 and H2A.X antibodies in ME49\",\n      \"pmids\": [\"24417889\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single method, no functional perturbation\", \"Enzyme responsible for local H4K20me1 not linked in this study\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"ME49\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Whether the globular-domain residue H4K31 carries regulatory information addressed a novel axis of chromatin control; showing H4K31ac marks active promoters while H4K31me1 populates active gene bodies but inversely tracks transcription established a bifunctional, position-dependent mark.\",\n      \"evidence\": \"ChIP-seq and mass spectrometry with genome-wide transcription correlation across Toxoplasma and Plasmodium\",\n      \"pmids\": [\"29101771\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Writers/erasers for H4K31 modifications not identified\", \"Mechanism reconciling gene-body H4K31me1 enrichment with transcriptional repression unresolved\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Whether TgH4 has a role beyond chromatin addressed a potential host-interaction function; recombinant TgH4 binding and modulating macrophage responses raised an extracellular immunomodulatory activity.\",\n      \"evidence\": \"IFA binding assay plus flow cytometry and ELISA on Ana-1 macrophages exposed to recombinant TgH4\",\n      \"pmids\": [\"29722109\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Recombinant protein applied exogenously with no genetic evidence of native extracellular secretion\", \"Single method per readout, no in vivo confirmation\", \"Receptor mediating macrophage binding not identified\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether global H4 acetylation is functionally linked to parasite replication addressed the physiological importance of the acetylation balance; HDAC inhibition raising H4ac and blocking endodyogeny connected the mark to cell-cycle progression.\",\n      \"evidence\": \"Western blot for H4 acetylation and fluorescence/electron microscopy of budding defects after Tubastatin A treatment in RH and ME49\",\n      \"pmids\": [\"33360687\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Pharmacological perturbation lacks genetic specificity for H4 versus other HDAC substrates\", \"Direct causal chain from H4ac to budding machinery not defined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"RH\"}, {\"species\": \"Toxoplasma gondii\", \"strain\": \"ME49\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The writers and erasers for H4K31 modifications, the genetic requirement of TgMYST-A and Set8-related methyltransferases for defined H4 marks in vivo, and the mechanistic basis of any native extracellular H4 function remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No enzyme assigned to H4K31 acetylation or monomethylation\", \"No genetic loss-of-function tying specific H4 marks to phenotypes\", \"Native secretion and receptor for extracellular TgH4 unknown\"],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0030527\", \"supporting_discovery_ids\": [1, 2, 3, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000786\", \"supporting_discovery_ids\": [2, 3, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0005721\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0000783\", \"supporting_discovery_ids\": [0, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"ME49\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006325\", \"supporting_discovery_ids\": [0, 1, 2, 4], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0006342\", \"supporting_discovery_ids\": [0, 3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0045814\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TgMYST-A (MYST-family histone acetyltransferase, acetylates H4 K5/K8/K12/K16)\",\n      \"Set8-related histone methyltransferase (mono/di/trimethylates H4K20)\",\n      \"histone variant H2A.X (co-enriched at subtelomeric heterochromatin)\"\n    ],\n    \"other_free_text\": [\n      \"H4ac and H4K31ac mark active promoters; H4K31me1 marks active gene bodies but inversely correlates with transcription.\",\n      \"H4K20me1/2/3 and H4K20me1 with H2A.X mark silent pericentric, telomeric, and subtelomeric-like heterochromatin.\",\n      \"Global H4 acetylation balance is coupled to endodyogeny; HDAC inhibition (Tubastatin A) raises H4ac and impairs daughter-cell budding.\",\n      \"Recombinant extracellular TgH4 binds murine macrophages and modulates TLR4 expression, chemotaxis, apoptosis, phagocytosis, and cytokine/NO secretion in vitro (Low confidence).\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_239260","name":null,"product":"histone H4","uniprot_acc":"A0A125YHU4","chromosome":"TGME49_chrVI","start_pos":496842},{"strain":"GT1","gene_id":"TGGT1_239260","name":null,"product":"histone H4","uniprot_acc":null,"chromosome":"TGGT1_chrVI","start_pos":491746},{"strain":"RH88","gene_id":"TGRH88_031680","name":null,"product":"histone H4","uniprot_acc":null,"chromosome":"CM023087","start_pos":3203749},{"strain":"VEG","gene_id":"TGVEG_239260","name":null,"product":"histone H4","uniprot_acc":"B9PNK6","chromosome":"TGVEG_chrVI","start_pos":511313}]}