identifier: traitmech:000510 label: MspJI system definition: A type IV modification-dependent restriction system in which an organism possesses an MspJI-family Mrr-like locus encoding a restriction endonuclease that recognizes methylcytosine- or hydroxymethylcytosine-modified DNA and cleaves both strands at a fixed distance from the modified cytosine. definition_source: DOI:10.1073/pnas.1018448108 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000496 synonyms: - synonym_text: MspJI synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1073/pnas.1018448108 snippet: MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. notes: Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target. - reference: DOI:10.1073/pnas.1018448108 snippet: All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine. notes: Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases. - reference: DOI:10.1093/nar/gkq327 snippet: Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine. notes: Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved. - reference: DOI:10.1093/nar/gkt747 snippet: The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. notes: Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| MspJI | 10\.1073/pnas\.1018448108 | The MspJI family of modification-dependent restriction endonucleases for epigenetic studies | ' notes: The pinned DefenseFinder article registry maps the MspJI source key to the Cohen-Karni et al. MspJI-family paper. causal_graphs: - graph_id: mspji_restricts_modified_cytosine_dna title: MspJI restricts modified-cytosine DNA description: Conservative system-level sketch linking an MspJI-family locus to modified-cytosine DNA restriction and to the Type IV restriction parent trait. scope_status: NONMECHANISTIC scope_notes: The graph captures MspJI as a named Mrr-like Type IV modification-dependent restriction family while leaving natural host breadth, exact sequence-context specificity across characterized homologs, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping unresolved. nodes: - node_id: mspji_family_locus label: MspJI-family locus node_type: GENETIC_ELEMENT description: A locus encoding an MspJI-family modification-dependent restriction endonuclease. - node_id: mspji_modified_cytosine_dna label: MspJI-targeted modified-cytosine DNA node_type: ENVIRONMENTAL_FACTOR description: DNA containing methylcytosine or hydroxymethylcytosine in an MspJI-family sequence context. - node_id: mspji_modified_cytosine_restriction label: MspJI modified-cytosine restriction node_type: BIOLOGICAL_PROCESS description: Modification-dependent restriction of C5-modified-cytosine DNA by an MspJI-family endonuclease. - node_id: mspji_system_trait label: MspJI system node_type: TRAIT grounding: traitmech:000510 description: Possession of a genome-encoded MspJI-family modification-dependent restriction system. - node_id: type_iv_modification_dependent_restriction label: type IV modification-dependent restriction system node_type: TRAIT grounding: traitmech:000496 description: Possession of a genome-encoded Type IV modification-dependent restriction system. edges: - subject: mspji_family_locus predicate: enables predicate_id: RO:0002327 object: mspji_modified_cytosine_restriction description: MspJI-family loci encode Mrr-like modification-dependent restriction endonucleases. evidence: - reference: DOI:10.1073/pnas.1018448108 snippet: MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. notes: Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target. - reference: DOI:10.1073/pnas.1018448108 snippet: All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine. notes: Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases. - subject: mspji_modified_cytosine_restriction predicate: mitigates predicate_id: METPO:2007407 object: mspji_modified_cytosine_dna description: MspJI-family restriction targets methylcytosine- or hydroxymethylcytosine-containing DNA. evidence: - reference: DOI:10.1073/pnas.1018448108 snippet: All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine. notes: Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases. - reference: DOI:10.1093/nar/gkq327 snippet: Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine. notes: Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved. - subject: mspji_modified_cytosine_restriction predicate: confers predicate_id: METPO:2007700 object: mspji_system_trait description: MspJI-family modified-cytosine restriction realizes the organism-level MspJI system possession trait. evidence: - reference: DOI:10.1093/nar/gkq327 snippet: Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine. notes: Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| MspJI | 10\.1073/pnas\.1018448108 | The MspJI family of modification-dependent restriction endonucleases for epigenetic studies | ' notes: The pinned DefenseFinder article registry maps the MspJI source key to the Cohen-Karni et al. MspJI-family paper. - subject: mspji_system_trait predicate: is a predicate_id: rdfs:subClassOf object: type_iv_modification_dependent_restriction description: MspJI system possession is a Type IV modification-dependent restriction system trait. evidence: - reference: DOI:10.1073/pnas.1018448108 snippet: MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. notes: Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target. - reference: DOI:10.1093/nar/gkt747 snippet: The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I-III. notes: Loenen and Raleigh define the Type IV class as modification-dependent restriction enzymes. discussions: - discussion_id: mspji-defensefinder-model-gap prompt: Resolve MspJI-family breadth, methylcytosine and hydroxymethylcytosine sequence-context specificity across natural hosts, accession-level protein examples, and DefenseFinder RM_Type_IV HMM/rules mapping before minting narrower MspJI mechanism or component traits. kind: KNOWLEDGE_GAP status: OPEN rationale: Zheng et al. support MspJI as a methylcytosine- and hydroxymethylcytosine-dependent restriction endonuclease, Cohen-Karni et al. support MspJI homologs as a family of C5-modified-cytosine-dependent restriction endonucleases, and the pinned DefenseFinder article registry maps MspJI to the Cohen-Karni et al. paper. The pinned HMM inventory and rules table have no exact MspJI rows. This first-pass record therefore does not resolve a reusable DefenseFinder profile model, exact accession-level protein examples, the breadth of MspJI-like systems across natural hosts, or the complete set of natural methylcytosine and hydroxymethylcytosine sequence contexts. evidence: - reference: DOI:10.1073/pnas.1018448108 snippet: MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. notes: Cohen-Karni et al. support MspJI as a modification-dependent restriction endonuclease with distance-defined cleavage relative to its modified target. - reference: DOI:10.1073/pnas.1018448108 snippet: All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine. notes: Cohen-Karni et al. biochemically characterized MspJI homologs and support the MspJI family as C5-modified-cytosine-dependent restriction endonucleases. - reference: DOI:10.1093/nar/gkq327 snippet: Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine. notes: Zheng et al. support MspJI restriction of both methylcytosine- and hydroxymethylcytosine-containing DNA while leaving glucosylated hydroxymethylcytosine DNA uncleaved. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| MspJI | 10\.1073/pnas\.1018448108 | The MspJI family of modification-dependent restriction endonucleases for epigenetic studies | ' notes: The pinned DefenseFinder article registry maps the MspJI source key to the Cohen-Karni et al. MspJI-family paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md notes: A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact MspJI row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: A structured first-pass search of the pinned DefenseFinder rules table found no exact MspJI system row. attaches_to: - causal_graphs#mspji_restricts_modified_cytosine_dna posed_by: codex posed_date: '2026-10-01' curation_history: - timestamp: '2026-10-01T08:04:00Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted MspJI system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the type IV modification-dependent restriction system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v387. llm_assisted: true - timestamp: '2026-10-01T08:04:02Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: Reviewed MspJI system during initial curation and left canonical_examples empty because Zheng et al. and Cohen-Karni et al. support MspJI and MspJI-family enzymes, but not a single stable NCBITaxon strain exemplar or accession-level protein example for the organism-level MspJI system trait. No paid research was used. llm_assisted: true