{"gene":"PF3D7_1322100","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2013,"finding":"SET2 (PfSETvs) controls histone H3 lysine 36 trimethylation (H3K36me3) on var genes; knockout of SET2 results in transcription of virtually all var genes in single parasite nuclei and their expression as proteins on the surface of infected red blood cells, establishing SET2 as the writer responsible for H3K36me3-dependent silencing of var genes.","method":"Gene knockout, ChIP, RNA-seq, flow cytometry (surface protein expression)","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function with multiple orthogonal readouts (ChIP for H3K36me3, transcriptomics, surface protein assay); independently replicated in subsequent studies","pmids":["23823717"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"SET2 (PfSETvs)-dependent H3K36me3 is present along the entire var gene body, including the transcription start site; low occupancy of SET2 at the transcription start site and intronic promoter coincides with antisense long non-coding RNA transcription and var gene expression.","method":"ChIP-seq, RNA-seq, gene knockout","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — ChIP-seq genome-wide occupancy data combined with genetic knockout, single rigorous study with multiple orthogonal methods","pmids":["23823717"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"SET2 (PfSET2) is recruited to var gene loci through direct interaction with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II; this interaction is inconsistent with recruitment during mRNA synthesis and instead is linked to non-coding RNA transcription at both active and silent var loci.","method":"Co-immunoprecipitation, dominant-negative overexpression, ChIP","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding interaction shown by Co-IP and functional consequence confirmed by dominant-negative overexpression inducing var switching; single lab","pmids":["24391504"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"SET2 (PfSET2) binds specifically to the unphosphorylated form of the RNA Pol II CTD; overexpression of a dominant-negative form of SET2 designed to disrupt RNA Pol II binding induced rapid var gene expression switching, confirming both a role for RNA Pol II in SET2 recruitment and SET2's function in var gene regulation.","method":"Dominant-negative overexpression, var gene switching assay, Co-IP","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — dominant-negative functional experiment with direct phenotypic readout (switching rate), Co-IP for binding specificity; single lab","pmids":["24391504"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"H3K36me3 (the epigenetic mark deposited by SET2/PfSET2) is enriched at both active and silent var gene loci, indicating that SET2 recruitment and mark deposition are not restricted to transcriptionally active genes.","method":"ChIP-seq","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide ChIP-seq data, single lab","pmids":["24391504"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"SET2 (PfSET2) contains a PHD (Plant Homeodomain)-like domain that specifically binds the H3K36me2 mark (an intermediate product of H3K36me3 formation on nucleosomes), and this PHD–H3K36me2 interaction allosterically stimulates the SET2 catalytic domain activity on nucleosome substrates, suggesting a mechanism for propagation of H3K36me3 across all var gene loci.","method":"In vitro binding assay (PHD domain vs. H3K36me2 peptide/nucleosome), in vitro histone methyltransferase activity assay, domain mutagenesis/truncation","journal":"Biochimica et biophysica acta. Gene regulatory mechanisms","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro enzymatic reconstitution with nucleosome substrates demonstrating allosteric stimulation; single lab, single study","pmids":["34389510"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"Deletion of SET2 (PfSET2) leads to marked reduction of both intrachromosomal and interchromosomal chromatin interactions at high-interacting regions (HIRs) enriched with H3K36me3 and H3K9me3 at telomeres and var gene loci, and this chromatin reorganization correlates with transcriptional activation of var genes; different var gene clusters show distinct transcriptional activation potential upon SET2 deletion.","method":"Hi-C (3D genome organization), ChIP-seq, RNA-seq, CRISPR/Cas9 gene deletion","journal":"Microbiology spectrum","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic deletion combined with genome-wide Hi-C, ChIP-seq, and RNA-seq; multiple orthogonal methods in a single rigorous study","pmids":["36602337"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"finding":"SET2 (identified as a putative epigenetic regulator) localizes to distinct nuclear sub-compartments in P. falciparum, with punctate distribution in perinuclear sub-compartments consistent with a role in virulence gene regulation.","method":"GFP/HA tagging, fluorescence microscopy, subcellular fractionation","journal":"International journal for parasitology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization by fluorescence tagging only; no direct functional consequence demonstrated in this study for SET2 specifically","pmids":["19765590"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"SET2 (PfSET2/PfSETvs; PF3D7_1322100) is a histone-lysine N-methyltransferase that deposits H3K36me3 across the bodies of var genes in P. falciparum; it is recruited to var loci via direct interaction with the unphosphorylated CTD of RNA Pol II (likely during non-coding RNA transcription), and an internal PHD-like domain that reads H3K36me2 allosterically stimulates its catalytic activity to propagate the H3K36me3 mark; this mark maintains a repressive 3D chromatin architecture (high-interacting regions at telomeres and var loci), and loss of SET2 collapses these chromatin interactions and derepresses virtually all var genes simultaneously."},"narrative":{"mechanistic_narrative":"SET2 (PF3D7_1322100) is the histone-lysine N-methyltransferase that writes H3K36 trimethylation across var gene loci in Plasmodium falciparum and thereby enforces mutually exclusive silencing of this virulence-associated gene family [PMID:23823717]. H3K36me3 spans the entire var gene body, and knockout of SET2 abolishes this mark and derepresses virtually all var genes simultaneously, driving their expression as surface proteins on infected erythrocytes [PMID:23823717]. SET2 is recruited to var loci through direct binding to the unphosphorylated C-terminal domain of RNA polymerase II — an interaction linked to non-coding rather than mRNA transcription — such that dominant-negative disruption of this contact triggers rapid var gene switching [PMID:24391504]. The mark is deposited at both active and silent var loci, and an internal PHD-like domain that reads the H3K36me2 intermediate allosterically stimulates the SET2 catalytic domain on nucleosomes, providing a mechanism for spreading H3K36me3 across the family [PMID:24391504, PMID:34389510]. At the genome-organization level, SET2-dependent H3K36me3 sustains high-interacting chromatin regions at telomeres and var clusters, and its deletion collapses these intra- and interchromosomal interactions in concert with var activation [PMID:36602337].","teleology":[{"year":2013,"claim":"Establishing which enzyme controls var gene silencing addressed how the parasite achieves mutually exclusive expression of its virulence gene family; SET2 was identified as the H3K36me3 writer whose loss derepresses nearly all var genes.","evidence":"Gene knockout with ChIP, RNA-seq and surface protein flow cytometry in P. falciparum","pmids":["23823717"],"confidence":"High","gaps":["Does not resolve how a single active var gene escapes silencing","Mechanism of mark deposition timing across the cell cycle not addressed"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"Mapping the H3K36me3 distribution clarified where SET2 acts, showing the mark covers the full var gene body and that reduced occupancy near the transcription start site and intronic promoter coincides with antisense lncRNA and var activation.","evidence":"Genome-wide ChIP-seq and RNA-seq with knockout in P. falciparum","pmids":["23823717"],"confidence":"High","gaps":["Causal direction between antisense lncRNA and loss of SET2 occupancy unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"claim":"How SET2 is targeted to var loci was addressed by showing it binds the unphosphorylated RNA Pol II CTD, linking recruitment to non-coding transcription and demonstrating functional relevance via dominant-negative-induced switching.","evidence":"Co-IP, dominant-negative overexpression with var switching assay, and ChIP in P. falciparum","pmids":["24391504"],"confidence":"Medium","gaps":["Single lab; reciprocal validation of the Pol II interaction limited","Nature of the non-coding transcript directing recruitment not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"claim":"Determining that H3K36me3 is present at both active and silent var loci showed SET2 recruitment and mark deposition are not gated by transcriptional state, refining the silencing model.","evidence":"Genome-wide ChIP-seq in P. falciparum","pmids":["24391504"],"confidence":"Medium","gaps":["Does not explain how identical mark levels yield different transcriptional outcomes at active versus silent loci"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"The biochemical basis for spreading H3K36me3 was addressed by showing a SET2 PHD-like domain reads the H3K36me2 intermediate and allosterically boosts catalytic activity on nucleosomes.","evidence":"In vitro binding and histone methyltransferase assays with domain mutagenesis/truncation on nucleosome substrates in P. falciparum","pmids":["34389510"],"confidence":"Medium","gaps":["Single in vitro study; allosteric propagation not demonstrated in vivo","Structural basis of PHD–H3K36me2 recognition not resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"Whether SET2 shapes 3D genome architecture was addressed by showing its deletion collapses intra- and interchromosomal interactions at telomeric and var high-interacting regions, coupling chromatin reorganization to var activation.","evidence":"Hi-C, ChIP-seq, RNA-seq and CRISPR/Cas9 deletion in P. falciparum","pmids":["36602337"],"confidence":"High","gaps":["Does not establish whether architectural change is cause or consequence of transcriptional activation","Basis for distinct activation potential among var clusters unexplained"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"How the single active var gene evades SET2-mediated silencing while the mark blankets the rest of the family remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No mechanism linking non-coding transcript identity to selective SET2 exclusion at the active locus","In vivo confirmation of PHD-driven mark propagation lacking"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["RNA POLYMERASE II (UNPHOSPHORYLATED CTD)"],"other_free_text":["Writes H3K36me3 across the full body of var genes to enforce their silencing [#0, #1]","Recruited to var loci via direct binding to the unphosphorylated RNA Pol II CTD, linked to non-coding RNA transcription [#2, #3]","H3K36me3 present at both active and silent var loci [#4]","PHD-like domain reads H3K36me2 and allosterically stimulates catalysis on nucleosomes [#5]","Maintains high-interacting chromatin regions at telomeres and var clusters; deletion collapses these interactions and activates var genes [#6]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"23823717","id":"PMC_23823717","title":"PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum.","date":"2013","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/23823717","citation_count":202,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18299133","id":"PMC_18299133","title":"Histone lysine methyltransferases and demethylases in Plasmodium falciparum.","date":"2008","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18299133","citation_count":106,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19765590","id":"PMC_19765590","title":"Potential epigenetic regulatory proteins localise to distinct nuclear sub-compartments in Plasmodium falciparum.","date":"2009","source":"International journal for parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/19765590","citation_count":65,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24391504","id":"PMC_24391504","title":"Recruitment of PfSET2 by RNA polymerase II to variant antigen encoding loci contributes to antigenic variation in P. falciparum.","date":"2014","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/24391504","citation_count":59,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SET2","PfSET2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27066899","id":"PMC_27066899","title":"A redesigned CRISPR/Cas9 system for marker-free genome editing in Plasmodium falciparum.","date":"2016","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/27066899","citation_count":26,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfSET2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34389510","id":"PMC_34389510","title":"Plasmodium falciparum SET2 domain is allosterically regulated by its PHD-like domain to methylate at H3K36.","date":"2021","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/34389510","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SET2","PfSET2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36602337","id":"PMC_36602337","title":"PfSET2 Is Involved in Genome Organization of Var Gene Family in Plasmodium falciparum.","date":"2023","source":"Microbiology spectrum","url":"https://pubmed.ncbi.nlm.nih.gov/36602337","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfSET2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6738,"output_tokens":2151,"usd":0.026239,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7477,"output_tokens":2672,"usd":0.052092,"stage2_stop_reason":"end_turn"},"total_usd":0.078331,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"SET2 (PfSETvs) controls histone H3 lysine 36 trimethylation (H3K36me3) on var genes; knockout of SET2 results in transcription of virtually all var genes in single parasite nuclei and their expression as proteins on the surface of infected red blood cells, establishing SET2 as the writer responsible for H3K36me3-dependent silencing of var genes.\",\n      \"method\": \"Gene knockout, ChIP, RNA-seq, flow cytometry (surface protein expression)\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function with multiple orthogonal readouts (ChIP for H3K36me3, transcriptomics, surface protein assay); independently replicated in subsequent studies\",\n      \"pmids\": [\"23823717\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"SET2 (PfSETvs)-dependent H3K36me3 is present along the entire var gene body, including the transcription start site; low occupancy of SET2 at the transcription start site and intronic promoter coincides with antisense long non-coding RNA transcription and var gene expression.\",\n      \"method\": \"ChIP-seq, RNA-seq, gene knockout\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — ChIP-seq genome-wide occupancy data combined with genetic knockout, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"23823717\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SET2 (PfSET2) is recruited to var gene loci through direct interaction with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II; this interaction is inconsistent with recruitment during mRNA synthesis and instead is linked to non-coding RNA transcription at both active and silent var loci.\",\n      \"method\": \"Co-immunoprecipitation, dominant-negative overexpression, ChIP\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding interaction shown by Co-IP and functional consequence confirmed by dominant-negative overexpression inducing var switching; single lab\",\n      \"pmids\": [\"24391504\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SET2 (PfSET2) binds specifically to the unphosphorylated form of the RNA Pol II CTD; overexpression of a dominant-negative form of SET2 designed to disrupt RNA Pol II binding induced rapid var gene expression switching, confirming both a role for RNA Pol II in SET2 recruitment and SET2's function in var gene regulation.\",\n      \"method\": \"Dominant-negative overexpression, var gene switching assay, Co-IP\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — dominant-negative functional experiment with direct phenotypic readout (switching rate), Co-IP for binding specificity; single lab\",\n      \"pmids\": [\"24391504\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"H3K36me3 (the epigenetic mark deposited by SET2/PfSET2) is enriched at both active and silent var gene loci, indicating that SET2 recruitment and mark deposition are not restricted to transcriptionally active genes.\",\n      \"method\": \"ChIP-seq\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide ChIP-seq data, single lab\",\n      \"pmids\": [\"24391504\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SET2 (PfSET2) contains a PHD (Plant Homeodomain)-like domain that specifically binds the H3K36me2 mark (an intermediate product of H3K36me3 formation on nucleosomes), and this PHD–H3K36me2 interaction allosterically stimulates the SET2 catalytic domain activity on nucleosome substrates, suggesting a mechanism for propagation of H3K36me3 across all var gene loci.\",\n      \"method\": \"In vitro binding assay (PHD domain vs. H3K36me2 peptide/nucleosome), in vitro histone methyltransferase activity assay, domain mutagenesis/truncation\",\n      \"journal\": \"Biochimica et biophysica acta. Gene regulatory mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro enzymatic reconstitution with nucleosome substrates demonstrating allosteric stimulation; single lab, single study\",\n      \"pmids\": [\"34389510\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Deletion of SET2 (PfSET2) leads to marked reduction of both intrachromosomal and interchromosomal chromatin interactions at high-interacting regions (HIRs) enriched with H3K36me3 and H3K9me3 at telomeres and var gene loci, and this chromatin reorganization correlates with transcriptional activation of var genes; different var gene clusters show distinct transcriptional activation potential upon SET2 deletion.\",\n      \"method\": \"Hi-C (3D genome organization), ChIP-seq, RNA-seq, CRISPR/Cas9 gene deletion\",\n      \"journal\": \"Microbiology spectrum\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic deletion combined with genome-wide Hi-C, ChIP-seq, and RNA-seq; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"36602337\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SET2 (identified as a putative epigenetic regulator) localizes to distinct nuclear sub-compartments in P. falciparum, with punctate distribution in perinuclear sub-compartments consistent with a role in virulence gene regulation.\",\n      \"method\": \"GFP/HA tagging, fluorescence microscopy, subcellular fractionation\",\n      \"journal\": \"International journal for parasitology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization by fluorescence tagging only; no direct functional consequence demonstrated in this study for SET2 specifically\",\n      \"pmids\": [\"19765590\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"SET2 (PfSET2/PfSETvs; PF3D7_1322100) is a histone-lysine N-methyltransferase that deposits H3K36me3 across the bodies of var genes in P. falciparum; it is recruited to var loci via direct interaction with the unphosphorylated CTD of RNA Pol II (likely during non-coding RNA transcription), and an internal PHD-like domain that reads H3K36me2 allosterically stimulates its catalytic activity to propagate the H3K36me3 mark; this mark maintains a repressive 3D chromatin architecture (high-interacting regions at telomeres and var loci), and loss of SET2 collapses these chromatin interactions and derepresses virtually all var genes simultaneously.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SET2 (PF3D7_1322100) is the histone-lysine N-methyltransferase that writes H3K36 trimethylation across var gene loci in Plasmodium falciparum and thereby enforces mutually exclusive silencing of this virulence-associated gene family [#0]. H3K36me3 spans the entire var gene body, and knockout of SET2 abolishes this mark and derepresses virtually all var genes simultaneously, driving their expression as surface proteins on infected erythrocytes [#0, #1]. SET2 is recruited to var loci through direct binding to the unphosphorylated C-terminal domain of RNA polymerase II — an interaction linked to non-coding rather than mRNA transcription — such that dominant-negative disruption of this contact triggers rapid var gene switching [#2, #3]. The mark is deposited at both active and silent var loci, and an internal PHD-like domain that reads the H3K36me2 intermediate allosterically stimulates the SET2 catalytic domain on nucleosomes, providing a mechanism for spreading H3K36me3 across the family [#4, #5]. At the genome-organization level, SET2-dependent H3K36me3 sustains high-interacting chromatin regions at telomeres and var clusters, and its deletion collapses these intra- and interchromosomal interactions in concert with var activation [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Establishing which enzyme controls var gene silencing addressed how the parasite achieves mutually exclusive expression of its virulence gene family; SET2 was identified as the H3K36me3 writer whose loss derepresses nearly all var genes.\",\n      \"evidence\": \"Gene knockout with ChIP, RNA-seq and surface protein flow cytometry in P. falciparum\",\n      \"pmids\": [\"23823717\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not resolve how a single active var gene escapes silencing\", \"Mechanism of mark deposition timing across the cell cycle not addressed\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Mapping the H3K36me3 distribution clarified where SET2 acts, showing the mark covers the full var gene body and that reduced occupancy near the transcription start site and intronic promoter coincides with antisense lncRNA and var activation.\",\n      \"evidence\": \"Genome-wide ChIP-seq and RNA-seq with knockout in P. falciparum\",\n      \"pmids\": [\"23823717\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causal direction between antisense lncRNA and loss of SET2 occupancy unresolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"How SET2 is targeted to var loci was addressed by showing it binds the unphosphorylated RNA Pol II CTD, linking recruitment to non-coding transcription and demonstrating functional relevance via dominant-negative-induced switching.\",\n      \"evidence\": \"Co-IP, dominant-negative overexpression with var switching assay, and ChIP in P. falciparum\",\n      \"pmids\": [\"24391504\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; reciprocal validation of the Pol II interaction limited\", \"Nature of the non-coding transcript directing recruitment not defined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Determining that H3K36me3 is present at both active and silent var loci showed SET2 recruitment and mark deposition are not gated by transcriptional state, refining the silencing model.\",\n      \"evidence\": \"Genome-wide ChIP-seq in P. falciparum\",\n      \"pmids\": [\"24391504\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not explain how identical mark levels yield different transcriptional outcomes at active versus silent loci\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The biochemical basis for spreading H3K36me3 was addressed by showing a SET2 PHD-like domain reads the H3K36me2 intermediate and allosterically boosts catalytic activity on nucleosomes.\",\n      \"evidence\": \"In vitro binding and histone methyltransferase assays with domain mutagenesis/truncation on nucleosome substrates in P. falciparum\",\n      \"pmids\": [\"34389510\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single in vitro study; allosteric propagation not demonstrated in vivo\", \"Structural basis of PHD–H3K36me2 recognition not resolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether SET2 shapes 3D genome architecture was addressed by showing its deletion collapses intra- and interchromosomal interactions at telomeric and var high-interacting regions, coupling chromatin reorganization to var activation.\",\n      \"evidence\": \"Hi-C, ChIP-seq, RNA-seq and CRISPR/Cas9 deletion in P. falciparum\",\n      \"pmids\": [\"36602337\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not establish whether architectural change is cause or consequence of transcriptional activation\", \"Basis for distinct activation potential among var clusters unexplained\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the single active var gene evades SET2-mediated silencing while the mark blankets the rest of the family remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanism linking non-coding transcript identity to selective SET2 exclusion at the active locus\", \"In vivo confirmation of PHD-driven mark propagation lacking\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0046975\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"GO:0140030\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006342\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"GO:0006338\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RNA polymerase II (unphosphorylated CTD)\"],\n    \"other_free_text\": [\n      \"Writes H3K36me3 across the full body of var genes to enforce their silencing [#0, #1]\",\n      \"Recruited to var loci via direct binding to the unphosphorylated RNA Pol II CTD, linked to non-coding RNA transcription [#2, #3]\",\n      \"H3K36me3 present at both active and silent var loci [#4]\",\n      \"PHD-like domain reads H3K36me2 and allosterically stimulates catalysis on nucleosomes [#5]\",\n      \"Maintains high-interacting chromatin regions at telomeres and var clusters; deletion collapses these interactions and activates var genes [#6]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1322100","name":null,"product":"histone-lysine N-methyltransferase SET2","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1206700","name":null,"product":"histone-lysine N-methyltransferase SET2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"SET2","evaluation":null}