{"gene":"THUMPD2","run_date":"2026-04-28T21:42:59","timeline":{"discoveries":[{"year":2023,"finding":"THUMPD2 was identified as a direct interaction partner of the co-factor TRMT112 in human cells, and was demonstrated to be an active N2-methylguanosine (m2G) methyltransferase that directly associates with U6 snRNA and is required for m2G modification of U6 snRNA, with a consequent role in pre-mRNA splicing.","method":"TRMT112 interaction network mapping in intact cells; biochemical demonstration of m2G MTase activity; direct association with U6 snRNA shown experimentally","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods (interactome, enzymatic activity assay, RNA association), replicated independently in a second paper (PMID:38165050)","pmids":["37283053"],"is_preprint":false},{"year":2021,"finding":"THUMPD2 was identified as one of seven methyltransferases pulled down as interaction partners of TRMT112 in a SILAC screen, and TRMT112 was shown to stabilize THUMPD2 in cells; a mutual feedback loop between TRMT112 and its MTase partners (including THUMPD2) was demonstrated.","method":"SILAC-based affinity pulldown; co-expression stability assays; single amino acid mutagenesis of TRMT112 surface","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal SILAC pulldown with mutagenesis, single lab","pmids":["34948388"],"is_preprint":false},{"year":2024,"finding":"THUMPD2 is the methyltransferase responsible for N2-methylguanosine (m2G) at position G72 of U6 snRNA (the catalytic center of the spliceosome) by explicitly recognizing U6-specific sequences and structural elements; THUMPD2 knockout eliminated U6 m2G72, impaired pre-mRNA splicing activity, caused thousands of altered alternative splicing events, activated nonsense-mediated mRNA decay, and was associated with retinal degeneration and age-related macular degeneration.","method":"Genetic knockout of THUMPD2; mass spectrometry-based RNA modification mapping; transcriptome-wide alternative splicing analysis; NMD pathway activation assay; in vivo retinal function studies","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 — KO + RNA modification mapping + mechanistic pathway characterization + in vivo phenotype, replicated across two independent papers","pmids":["38165050"],"is_preprint":false},{"year":2001,"finding":"THUMPD2 (then called C2orf8 / 288L6 SAM-methyltransferase) was identified as a novel human gene containing three conserved S-adenosylmethionine-dependent methyltransferase motifs, localized to chromosome 2p22→p21, and shown to have multiple alternative transcripts with a shared coding region encoding a 244 amino acid protein.","method":"FISH chromosomal localization; RACE analysis; RT-PCR and Northern blot; bioinformatic ORF analysis","journal":"Cytogenetics and cell genetics","confidence":"Low","confidence_rationale":"Tier 3 — initial cloning/characterization with no functional enzymatic validation","pmids":["12063391"],"is_preprint":false},{"year":2019,"finding":"Knockdown of THUMPD2 via siRNA in human esophageal squamous cell carcinoma cells conferred resistance to both cisplatin and 5-fluorouracil, suggesting THUMPD2 plays a role in drug sensitivity.","method":"Transposon activation mutagenesis screen; siRNA knockdown; IC50 comparison between drug-resistant and wild-type cells","journal":"The journal of gene medicine","confidence":"Low","confidence_rationale":"Tier 3 — single lab, single method (siRNA KD), no mechanistic pathway placement","pmids":["31656051"],"is_preprint":false}],"current_model":"THUMPD2 is an S-adenosylmethionine-dependent N2-methylguanosine (m2G) methyltransferase that functions in complex with the co-factor TRMT112, specifically installs the m2G modification at position G72 of U6 snRNA by recognizing U6-specific sequences and structural elements, and thereby promotes efficient pre-mRNA splicing; loss of THUMPD2 eliminates U6 m2G72, causes widespread alternative splicing changes, activates nonsense-mediated mRNA decay, and leads to retinal degeneration in vivo."},"narrative":{"teleology":[{"year":2001,"claim":"Before any function was known, initial cloning revealed that THUMPD2 (then C2orf8) encodes a protein with three conserved SAM-dependent methyltransferase motifs, establishing it as a candidate RNA or protein methyltransferase.","evidence":"FISH localization, RACE, RT-PCR, Northern blot, and bioinformatic ORF analysis in human cells","pmids":["12063391"],"confidence":"Low","gaps":["No enzymatic activity demonstrated; motifs alone do not confirm function","Substrate identity unknown","No cellular phenotype assessed"]},{"year":2021,"claim":"Identification of THUMPD2 as a TRMT112 interaction partner, and demonstration that TRMT112 stabilizes THUMPD2 protein, placed THUMPD2 within the family of TRMT112-dependent methyltransferases and suggested it requires a co-factor for activity.","evidence":"SILAC-based affinity pulldown of TRMT112 interactors; co-expression stability assays and TRMT112 surface mutagenesis in human cells","pmids":["34948388"],"confidence":"Medium","gaps":["Catalytic activity of THUMPD2 not directly demonstrated","RNA substrate not identified","Biological consequence of disruption unknown"]},{"year":2023,"claim":"Direct demonstration that THUMPD2 is an active m2G methyltransferase that physically associates with U6 snRNA and requires TRMT112 answered the central question of substrate identity and enzymatic activity.","evidence":"TRMT112 interaction network mapping in intact cells; biochemical m2G methyltransferase activity assay; direct THUMPD2–U6 snRNA association","pmids":["37283053"],"confidence":"High","gaps":["Precise target nucleotide on U6 not yet pinpointed in this study","Splicing consequences not yet characterized genome-wide","Structural basis of U6 recognition unknown"]},{"year":2024,"claim":"Knockout studies pinpointed position G72 of U6 snRNA as the THUMPD2-dependent m2G site and revealed that loss of this single modification causes widespread alternative splicing defects, NMD activation, and retinal degeneration, establishing the physiological importance of U6 m2G72.","evidence":"THUMPD2 genetic knockout; mass spectrometry RNA modification mapping; transcriptome-wide splicing analysis; NMD pathway activation assay; in vivo retinal phenotyping","pmids":["38165050"],"confidence":"High","gaps":["Structural basis for THUMPD2 recognition of U6-specific sequences undetermined","Whether retinal degeneration results from specific mis-spliced transcripts or global splicing dysfunction is unresolved","Potential additional RNA substrates beyond U6 not excluded"]},{"year":null,"claim":"Key open questions include the structural mechanism by which THUMPD2–TRMT112 recognizes U6 snRNA, whether THUMPD2 modifies additional RNA targets, and which specific mis-spliced transcripts drive retinal degeneration.","evidence":"","pmids":[],"confidence":"High","gaps":["No crystal or cryo-EM structure of THUMPD2–TRMT112–U6 complex","Comprehensive substrate profiling beyond U6 snRNA not performed","Causal link between individual mis-spliced mRNAs and retinal disease phenotype not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,2,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,2]}],"localization":[],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2]}],"complexes":["THUMPD2–TRMT112"],"partners":["TRMT112"],"other_free_text":[]},"mechanistic_narrative":"THUMPD2 is an S-adenosylmethionine (SAM)-dependent methyltransferase that, in complex with the co-factor TRMT112, installs the N2-methylguanosine (m2G) modification at position G72 of U6 snRNA — a residue located within the catalytic center of the spliceosome [PMID:37283053, PMID:38165050]. TRMT112 stabilizes THUMPD2 protein levels and is required for its activity, and THUMPD2 recognizes U6-specific sequences and structural elements to achieve substrate specificity [PMID:34948388, PMID:38165050]. Genetic ablation of THUMPD2 eliminates U6 m2G72, causing thousands of alternative splicing changes and activation of nonsense-mediated mRNA decay, and leads to retinal degeneration in vivo, linking loss of this modification to age-related macular degeneration [PMID:38165050]."},"prefetch_data":{"uniprot":{"accession":"Q9BTF0","full_name":"U6 snRNA (guanine-N(2))-methyltransferase THUMPD2","aliases":["THUMP domain-containing protein 2"],"length_aa":503,"mass_kda":56.4,"function":"Catalytic subunit of the THUMPD2-TRM112 methyltransferase complex, that specifically mediates the S-adenosyl-L-methionine-dependent N(2)-methylation of guanosine nucleotides, most probably at position 72 (m2G72), in the U6snRNA of the major spliceosome (PubMed:37283053). This modification in the U6 snRNA affects the constitutive splicing efficiency of introns that have suboptimal splice sites and can impact final mRNA levels (PubMed:37283053)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9BTF0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/THUMPD2","classification":"Not Classified","n_dependent_lines":8,"n_total_lines":1208,"dependency_fraction":0.006622516556291391},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/THUMPD2","total_profiled":1310},"omim":[{"mim_id":"621532","title":"THUMP DOMAIN PROTEIN 3, tRNA GUANOSINE METHYLTRANSFERASE; THUMPD3","url":"https://www.omim.org/entry/621532"},{"mim_id":"618630","title":"tRNA METHYLTRANSFERASE SUBUNIT 11-2; TRMT112","url":"https://www.omim.org/entry/618630"},{"mim_id":"611751","title":"THUMP DOMAIN PROTEIN 2, tRNA and snRNA GUANOSINE METHYLTRANSFERASE; THUMPD2","url":"https://www.omim.org/entry/611751"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Nucleoplasm","reliability":"Uncertain"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/THUMPD2"},"hgnc":{"alias_symbol":["MGC2454"],"prev_symbol":["C2orf8"]},"alphafold":{"accession":"Q9BTF0","domains":[{"cath_id":"3.40.50.150","chopping":"285-420_474-498","consensus_level":"high","plddt":92.5528,"start":285,"end":498}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BTF0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BTF0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BTF0-F1-predicted_aligned_error_v6.png","plddt_mean":75.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=THUMPD2","jax_strain_url":"https://www.jax.org/strain/search?query=THUMPD2"},"sequence":{"accession":"Q9BTF0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BTF0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BTF0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BTF0"}},"corpus_meta":[{"pmid":"35685361","id":"PMC_35685361","title":"Integrative RNA profiling of TBEV-infected neurons and astrocytes reveals potential pathogenic effectors.","date":"2022","source":"Computational and structural biotechnology journal","url":"https://pubmed.ncbi.nlm.nih.gov/35685361","citation_count":30,"is_preprint":false},{"pmid":"37283053","id":"PMC_37283053","title":"N 2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing.","date":"2023","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/37283053","citation_count":27,"is_preprint":false},{"pmid":"34948388","id":"PMC_34948388","title":"Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34948388","citation_count":23,"is_preprint":false},{"pmid":"38165050","id":"PMC_38165050","title":"THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration.","date":"2024","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/38165050","citation_count":7,"is_preprint":false},{"pmid":"12063391","id":"PMC_12063391","title":"Localization, genomic organization, and alternative transcription of a novel human SAM-dependent methyltransferase gene on chromosome 2p22-->p21.","date":"2001","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12063391","citation_count":6,"is_preprint":false},{"pmid":"31656051","id":"PMC_31656051","title":"THUMP domain containing 2 protein possibly induces resistance to cisplatin and 5-fluorouracil in in vitro human esophageal squamous cell carcinoma cells as revealed by transposon activation mutagenesis.","date":"2019","source":"The journal of gene medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31656051","citation_count":5,"is_preprint":false},{"pmid":"39071668","id":"PMC_39071668","title":"RNA-binding protein THUMPD2 inhibits proliferation and promotes metastasis in epithelial ovarian cancer.","date":"2024","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/39071668","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4958,"output_tokens":1315,"usd":0.017299},"stage2":{"model":"claude-opus-4-6","input_tokens":4540,"output_tokens":1454,"usd":0.088575},"total_usd":0.105874,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"THUMPD2 was identified as a direct interaction partner of the co-factor TRMT112 in human cells, and was demonstrated to be an active N2-methylguanosine (m2G) methyltransferase that directly associates with U6 snRNA and is required for m2G modification of U6 snRNA, with a consequent role in pre-mRNA splicing.\",\n      \"method\": \"TRMT112 interaction network mapping in intact cells; biochemical demonstration of m2G MTase activity; direct association with U6 snRNA shown experimentally\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (interactome, enzymatic activity assay, RNA association), replicated independently in a second paper (PMID:38165050)\",\n      \"pmids\": [\"37283053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"THUMPD2 was identified as one of seven methyltransferases pulled down as interaction partners of TRMT112 in a SILAC screen, and TRMT112 was shown to stabilize THUMPD2 in cells; a mutual feedback loop between TRMT112 and its MTase partners (including THUMPD2) was demonstrated.\",\n      \"method\": \"SILAC-based affinity pulldown; co-expression stability assays; single amino acid mutagenesis of TRMT112 surface\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal SILAC pulldown with mutagenesis, single lab\",\n      \"pmids\": [\"34948388\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"THUMPD2 is the methyltransferase responsible for N2-methylguanosine (m2G) at position G72 of U6 snRNA (the catalytic center of the spliceosome) by explicitly recognizing U6-specific sequences and structural elements; THUMPD2 knockout eliminated U6 m2G72, impaired pre-mRNA splicing activity, caused thousands of altered alternative splicing events, activated nonsense-mediated mRNA decay, and was associated with retinal degeneration and age-related macular degeneration.\",\n      \"method\": \"Genetic knockout of THUMPD2; mass spectrometry-based RNA modification mapping; transcriptome-wide alternative splicing analysis; NMD pathway activation assay; in vivo retinal function studies\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — KO + RNA modification mapping + mechanistic pathway characterization + in vivo phenotype, replicated across two independent papers\",\n      \"pmids\": [\"38165050\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"THUMPD2 (then called C2orf8 / 288L6 SAM-methyltransferase) was identified as a novel human gene containing three conserved S-adenosylmethionine-dependent methyltransferase motifs, localized to chromosome 2p22→p21, and shown to have multiple alternative transcripts with a shared coding region encoding a 244 amino acid protein.\",\n      \"method\": \"FISH chromosomal localization; RACE analysis; RT-PCR and Northern blot; bioinformatic ORF analysis\",\n      \"journal\": \"Cytogenetics and cell genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — initial cloning/characterization with no functional enzymatic validation\",\n      \"pmids\": [\"12063391\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Knockdown of THUMPD2 via siRNA in human esophageal squamous cell carcinoma cells conferred resistance to both cisplatin and 5-fluorouracil, suggesting THUMPD2 plays a role in drug sensitivity.\",\n      \"method\": \"Transposon activation mutagenesis screen; siRNA knockdown; IC50 comparison between drug-resistant and wild-type cells\",\n      \"journal\": \"The journal of gene medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, single method (siRNA KD), no mechanistic pathway placement\",\n      \"pmids\": [\"31656051\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"THUMPD2 is an S-adenosylmethionine-dependent N2-methylguanosine (m2G) methyltransferase that functions in complex with the co-factor TRMT112, specifically installs the m2G modification at position G72 of U6 snRNA by recognizing U6-specific sequences and structural elements, and thereby promotes efficient pre-mRNA splicing; loss of THUMPD2 eliminates U6 m2G72, causes widespread alternative splicing changes, activates nonsense-mediated mRNA decay, and leads to retinal degeneration in vivo.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"THUMPD2 is an S-adenosylmethionine (SAM)-dependent methyltransferase that, in complex with the co-factor TRMT112, installs the N2-methylguanosine (m2G) modification at position G72 of U6 snRNA — a residue located within the catalytic center of the spliceosome [PMID:37283053, PMID:38165050]. TRMT112 stabilizes THUMPD2 protein levels and is required for its activity, and THUMPD2 recognizes U6-specific sequences and structural elements to achieve substrate specificity [PMID:34948388, PMID:38165050]. Genetic ablation of THUMPD2 eliminates U6 m2G72, causing thousands of alternative splicing changes and activation of nonsense-mediated mRNA decay, and leads to retinal degeneration in vivo, linking loss of this modification to age-related macular degeneration [PMID:38165050].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Before any function was known, initial cloning revealed that THUMPD2 (then C2orf8) encodes a protein with three conserved SAM-dependent methyltransferase motifs, establishing it as a candidate RNA or protein methyltransferase.\",\n      \"evidence\": \"FISH localization, RACE, RT-PCR, Northern blot, and bioinformatic ORF analysis in human cells\",\n      \"pmids\": [\"12063391\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No enzymatic activity demonstrated; motifs alone do not confirm function\",\n        \"Substrate identity unknown\",\n        \"No cellular phenotype assessed\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identification of THUMPD2 as a TRMT112 interaction partner, and demonstration that TRMT112 stabilizes THUMPD2 protein, placed THUMPD2 within the family of TRMT112-dependent methyltransferases and suggested it requires a co-factor for activity.\",\n      \"evidence\": \"SILAC-based affinity pulldown of TRMT112 interactors; co-expression stability assays and TRMT112 surface mutagenesis in human cells\",\n      \"pmids\": [\"34948388\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Catalytic activity of THUMPD2 not directly demonstrated\",\n        \"RNA substrate not identified\",\n        \"Biological consequence of disruption unknown\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Direct demonstration that THUMPD2 is an active m2G methyltransferase that physically associates with U6 snRNA and requires TRMT112 answered the central question of substrate identity and enzymatic activity.\",\n      \"evidence\": \"TRMT112 interaction network mapping in intact cells; biochemical m2G methyltransferase activity assay; direct THUMPD2–U6 snRNA association\",\n      \"pmids\": [\"37283053\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Precise target nucleotide on U6 not yet pinpointed in this study\",\n        \"Splicing consequences not yet characterized genome-wide\",\n        \"Structural basis of U6 recognition unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Knockout studies pinpointed position G72 of U6 snRNA as the THUMPD2-dependent m2G site and revealed that loss of this single modification causes widespread alternative splicing defects, NMD activation, and retinal degeneration, establishing the physiological importance of U6 m2G72.\",\n      \"evidence\": \"THUMPD2 genetic knockout; mass spectrometry RNA modification mapping; transcriptome-wide splicing analysis; NMD pathway activation assay; in vivo retinal phenotyping\",\n      \"pmids\": [\"38165050\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for THUMPD2 recognition of U6-specific sequences undetermined\",\n        \"Whether retinal degeneration results from specific mis-spliced transcripts or global splicing dysfunction is unresolved\",\n        \"Potential additional RNA substrates beyond U6 not excluded\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include the structural mechanism by which THUMPD2–TRMT112 recognizes U6 snRNA, whether THUMPD2 modifies additional RNA targets, and which specific mis-spliced transcripts drive retinal degeneration.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No crystal or cryo-EM structure of THUMPD2–TRMT112–U6 complex\",\n        \"Comprehensive substrate profiling beyond U6 snRNA not performed\",\n        \"Causal link between individual mis-spliced mRNAs and retinal disease phenotype not established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0016740\",\n        \"supporting_discovery_ids\": [0, 2, 3]\n      },\n      {\n        \"term_id\": \"GO:0003723\",\n        \"supporting_discovery_ids\": [0, 2]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"R-HSA-8953854\",\n        \"supporting_discovery_ids\": [0, 2]\n      }\n    ],\n    \"complexes\": [\n      \"THUMPD2–TRMT112\"\n    ],\n    \"partners\": [\n      \"TRMT112\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}