{"gene":"TG_217350","gene_symbol":"METTL3","run_date":"2026-09-08T11:06:32","timeline":{"discoveries":[{"year":2021,"finding":"METTL3 functions as a component of the m6A methyltransferase complex in Toxoplasma gondii, and knockdown of METTL3 results in diminished m6A marks on mRNA transcripts and complete arrest of parasite replication.","method":"Knockdown (loss-of-function) with m6A mapping and parasite replication phenotypic readout","journal":"PLoS Pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean knockdown with two orthogonal readouts (m6A quantification and replication arrest), single lab","pmids":["34324585"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2021,"finding":"Loss of METTL3 leads to a defect in mRNA 3'-end formation (pre-mRNA cleavage and polyadenylation), establishing that m6A writing by METTL3 is required for proper 3'-end processing of pre-mRNAs in Toxoplasma gondii.","method":"Knockdown of METTL3 with analysis of transcript 3'-end formation; phenocopied by knockdown of WTAP and YTH1 (components of the same pathway)","journal":"PLoS Pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined molecular phenotype (3'-end processing defect), supported by pathway epistasis with WTAP and YTH1, single lab","pmids":["34324585"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2021,"finding":"METTL3 acts in complex with WTAP as part of the m6A methyltransferase machinery in Toxoplasma gondii; m6A marks deposited by this complex are preferentially located near the 3'-boundary of mRNAs and are read by YTH-domain proteins that are integral members of the cleavage and polyadenylation machinery.","method":"Identification of novel complex components, m6A transcriptome mapping, and functional characterization of YTH-domain reader proteins via Co-IP/interaction studies and knockdown","journal":"PLoS Pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — m6A mapping plus functional epistasis linking writer complex to reader proteins and 3'-end processing machinery, single lab","pmids":["34324585"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"In Toxoplasma gondii, METTL3 forms part of an m6A methyltransferase complex with WTAP that deposits m6A marks preferentially near the 3'-ends of mRNA transcripts; these marks are recognized by YTH-domain proteins integral to the cleavage and polyadenylation machinery, thereby coupling m6A writing to pre-mRNA 3'-end processing, and loss of METTL3 causes defective 3'-end formation and complete arrest of parasite replication."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii, METTL3 is the catalytic writer of an N6-methyladenosine (m6A) methyltransferase complex that couples mRNA methylation to pre-mRNA 3'-end processing and is essential for parasite replication [PMID:34324585]. METTL3 acts together with WTAP to deposit m6A marks that are preferentially positioned near the 3'-boundary of transcripts, where they are recognized by YTH-domain reader proteins that are integral components of the cleavage and polyadenylation machinery [PMID:34324585]. Loss of METTL3 diminishes m6A marks, disrupts mRNA 3'-end formation, and completely arrests replication, with knockdown of WTAP and the YTH reader YTH1 phenocopying the 3'-end processing defect [PMID:34324585]. Beyond this writer-complex-to-reader axis linking m6A to 3'-end processing, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2021,"claim":"Establishing whether m6A writing is functionally required in Toxoplasma, this work showed METTL3 is a component of the m6A methyltransferase complex whose loss abolishes m6A marks and blocks parasite replication.","evidence":"Knockdown loss-of-function with m6A mapping and replication phenotyping in T. gondii","pmids":["34324585"],"confidence":"Medium","gaps":["Catalytic activity of METTL3 not directly demonstrated in vitro","Direct RNA substrates not resolved from indirect replication effects"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2021,"claim":"To define the molecular consequence of m6A loss, METTL3 knockdown was shown to cause defective mRNA 3'-end formation, linking m6A deposition to pre-mRNA cleavage and polyadenylation.","evidence":"METTL3 knockdown with transcript 3'-end analysis, phenocopied by WTAP and YTH1 knockdown in T. gondii","pmids":["34324585"],"confidence":"Medium","gaps":["Direct mechanism by which m6A marks recruit the 3'-end processing machinery not resolved","Transcript specificity of the 3'-end defect not defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2021,"claim":"To connect writer to reader, METTL3 was shown to act with WTAP to place m6A near mRNA 3'-boundaries, marks that are read by YTH-domain proteins integral to the cleavage and polyadenylation machinery.","evidence":"Complex component identification, m6A transcriptome mapping, Co-IP/interaction studies and knockdown of YTH readers in T. gondii","pmids":["34324585"],"confidence":"Medium","gaps":["Stoichiometry and architecture of the METTL3-WTAP complex not determined","Direct physical contact between YTH readers and cleavage/polyadenylation factors not structurally defined"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"Whether METTL3's role in 3'-end processing is conserved beyond Toxoplasma and how m6A-marked transcripts are mechanistically routed to specific processing outcomes remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the METTL3 complex","Individual mRNA targets whose 3'-end processing depends on METTL3 not enumerated","Catalytic mechanism not reconstituted in vitro"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["m6A methyltransferase complex (METTL3-WTAP)"],"partners":["WTAP","YTH1 (YTH-DOMAIN READER)"],"other_free_text":["m6A marks deposited by the METTL3-WTAP complex are preferentially located near mRNA 3'-boundaries and are recognized by YTH-domain readers integral to the cleavage and polyadenylation machinery [#2].","METTL3 knockdown causes complete arrest of Toxoplasma gondii replication, indicating an essential role [#0]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"34324585","id":"PMC_34324585","title":"m6A RNA methylation facilitates pre-mRNA 3'-end formation and is essential for viability of Toxoplasma gondii.","date":"2021","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/34324585","citation_count":27,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2914,"output_tokens":900,"usd":0.011121,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5708,"output_tokens":1913,"usd":0.038183,"stage2_stop_reason":"end_turn"},"total_usd":0.049304,"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\": 2021,\n      \"finding\": \"METTL3 functions as a component of the m6A methyltransferase complex in Toxoplasma gondii, and knockdown of METTL3 results in diminished m6A marks on mRNA transcripts and complete arrest of parasite replication.\",\n      \"method\": \"Knockdown (loss-of-function) with m6A mapping and parasite replication phenotypic readout\",\n      \"journal\": \"PLoS Pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean knockdown with two orthogonal readouts (m6A quantification and replication arrest), single lab\",\n      \"pmids\": [\"34324585\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Loss of METTL3 leads to a defect in mRNA 3'-end formation (pre-mRNA cleavage and polyadenylation), establishing that m6A writing by METTL3 is required for proper 3'-end processing of pre-mRNAs in Toxoplasma gondii.\",\n      \"method\": \"Knockdown of METTL3 with analysis of transcript 3'-end formation; phenocopied by knockdown of WTAP and YTH1 (components of the same pathway)\",\n      \"journal\": \"PLoS Pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined molecular phenotype (3'-end processing defect), supported by pathway epistasis with WTAP and YTH1, single lab\",\n      \"pmids\": [\"34324585\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"METTL3 acts in complex with WTAP as part of the m6A methyltransferase machinery in Toxoplasma gondii; m6A marks deposited by this complex are preferentially located near the 3'-boundary of mRNAs and are read by YTH-domain proteins that are integral members of the cleavage and polyadenylation machinery.\",\n      \"method\": \"Identification of novel complex components, m6A transcriptome mapping, and functional characterization of YTH-domain reader proteins via Co-IP/interaction studies and knockdown\",\n      \"journal\": \"PLoS Pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — m6A mapping plus functional epistasis linking writer complex to reader proteins and 3'-end processing machinery, single lab\",\n      \"pmids\": [\"34324585\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"In Toxoplasma gondii, METTL3 forms part of an m6A methyltransferase complex with WTAP that deposits m6A marks preferentially near the 3'-ends of mRNA transcripts; these marks are recognized by YTH-domain proteins integral to the cleavage and polyadenylation machinery, thereby coupling m6A writing to pre-mRNA 3'-end processing, and loss of METTL3 causes defective 3'-end formation and complete arrest of parasite replication.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii, METTL3 is the catalytic writer of an N6-methyladenosine (m6A) methyltransferase complex that couples mRNA methylation to pre-mRNA 3'-end processing and is essential for parasite replication [#0]. METTL3 acts together with WTAP to deposit m6A marks that are preferentially positioned near the 3'-boundary of transcripts, where they are recognized by YTH-domain reader proteins that are integral components of the cleavage and polyadenylation machinery [#2]. Loss of METTL3 diminishes m6A marks, disrupts mRNA 3'-end formation, and completely arrests replication, with knockdown of WTAP and the YTH reader YTH1 phenocopying the 3'-end processing defect [#0, #1]. Beyond this writer-complex-to-reader axis linking m6A to 3'-end processing, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2021,\n      \"claim\": \"Establishing whether m6A writing is functionally required in Toxoplasma, this work showed METTL3 is a component of the m6A methyltransferase complex whose loss abolishes m6A marks and blocks parasite replication.\",\n      \"evidence\": \"Knockdown loss-of-function with m6A mapping and replication phenotyping in T. gondii\",\n      \"pmids\": [\"34324585\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Catalytic activity of METTL3 not directly demonstrated in vitro\", \"Direct RNA substrates not resolved from indirect replication effects\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"To define the molecular consequence of m6A loss, METTL3 knockdown was shown to cause defective mRNA 3'-end formation, linking m6A deposition to pre-mRNA cleavage and polyadenylation.\",\n      \"evidence\": \"METTL3 knockdown with transcript 3'-end analysis, phenocopied by WTAP and YTH1 knockdown in T. gondii\",\n      \"pmids\": [\"34324585\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Direct mechanism by which m6A marks recruit the 3'-end processing machinery not resolved\", \"Transcript specificity of the 3'-end defect not defined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"To connect writer to reader, METTL3 was shown to act with WTAP to place m6A near mRNA 3'-boundaries, marks that are read by YTH-domain proteins integral to the cleavage and polyadenylation machinery.\",\n      \"evidence\": \"Complex component identification, m6A transcriptome mapping, Co-IP/interaction studies and knockdown of YTH readers in T. gondii\",\n      \"pmids\": [\"34324585\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Stoichiometry and architecture of the METTL3-WTAP complex not determined\", \"Direct physical contact between YTH readers and cleavage/polyadenylation factors not structurally defined\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether METTL3's role in 3'-end processing is conserved beyond Toxoplasma and how m6A-marked transcripts are mechanistically routed to specific processing outcomes remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No structural model of the METTL3 complex\", \"Individual mRNA targets whose 3'-end processing depends on METTL3 not enumerated\", \"Catalytic mechanism not reconstituted in vitro\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016422\", \"supporting_discovery_ids\": [0, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0080009\", \"supporting_discovery_ids\": [0, 1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0031124\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"m6A methyltransferase complex (METTL3-WTAP)\"],\n    \"partners\": [\"WTAP\", \"YTH1 (YTH-domain reader)\"],\n    \"other_free_text\": [\n      \"m6A marks deposited by the METTL3-WTAP complex are preferentially located near mRNA 3'-boundaries and are recognized by YTH-domain readers integral to the cleavage and polyadenylation machinery [#2].\",\n      \"METTL3 knockdown causes complete arrest of Toxoplasma gondii replication, indicating an essential role [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_217350","name":"METTL3","product":"N6-adenosine-methyltransferase subunit METTL3","uniprot_acc":"A0A125YLJ5","chromosome":"TGME49_chrXII","start_pos":1764476},{"strain":"GT1","gene_id":"TGGT1_217350","name":null,"product":"putative methyltransferase MTA70","uniprot_acc":null,"chromosome":"TGGT1_chrXII","start_pos":1703631},{"strain":"RH88","gene_id":"TGRH88_059240","name":null,"product":"putative methyltransferase MTA70","uniprot_acc":null,"chromosome":"CM023093","start_pos":1775450},{"strain":"VEG","gene_id":"TGVEG_217350","name":null,"product":"putative methyltransferase MTA70","uniprot_acc":"B6KTX9","chromosome":"TGVEG_chrXII","start_pos":1737356}]}