From f7f7009db06744bfabc4fd4d9ddc149f0f18b7bf Mon Sep 17 00:00:00 2001 From: Pascale Gaudet Date: Fri, 29 Nov 2024 16:27:15 +0100 Subject: [PATCH] created new terms, fixes #29337, fixes #24912, Change modification-dependent protein binding & children to reader activity #27427 --- src/ontology/go-edit.obo | 88 +++++++++++++++++++++++++++++++++------- 1 file changed, 74 insertions(+), 14 deletions(-) diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index 8d56c759b8..d9412d032f 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -163668,7 +163668,7 @@ relationship: part_of GO:0044304 ! main axon id: GO:0030674 name: protein-macromolecule adaptor activity namespace: molecular_function -def: "The binding activity of a protein that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid." [GOC:bf, GOC:mah, GOC:vw] +def: "An adaptor activity that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid." [GOC:bf, GOC:mah, GOC:vw] subset: goslim_chembl subset: goslim_yeast synonym: "protein binding, bridging" EXACT [] @@ -359678,11 +359678,14 @@ creation_date: 2014-05-14T14:32:02Z [Term] id: GO:0061628 -name: H3K27me3 modified histone binding +name: H3K27me3 histone reader activity namespace: molecular_function -def: "Binding to a histone H3 in which the lysine residue at position 27 has been modified by trimethylation." [GOC:dph, PMID:23948251] -synonym: "H3-K27me3 modified histone binding" EXACT [GOC:dph] -is_a: GO:0035064 ! methylated histone binding +def: "A histone reader that recognizes a histone H3 trimethylated at lysine 27." [GOC:dph, PMID:23948251] +synonym: "H3-K27me3 modified histone binding" NARROW [] +synonym: "H3K27me3 modified histone binding" NARROW [] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI created_by: dph creation_date: 2014-05-14T15:36:53Z @@ -359892,7 +359895,7 @@ creation_date: 2014-10-02T15:26:53Z id: GO:0061649 name: ubiquitin-modified histone reader activity namespace: molecular_function -def: "A molecular adaptor that recognizes and binds a histone protein containing a ubiquitination modification and that brings the target protein into contact with another protein to allow those proteins to function in a coordinated way." [GOC:dph, PMID:24526689] +def: "A histone reader that recognizes a histone that bears a ubiquinated lysine residue." [GOC:dph, PMID:24526689] synonym: "ubiquitin modification-dependent histone binding" EXACT [] synonym: "ubiquitinated histone binding" RELATED [] is_a: GO:0140036 ! ubiquitin-modified protein reader activity @@ -364105,10 +364108,13 @@ creation_date: 2018-09-04T13:40:52Z [Term] id: GO:0062072 -name: H3K9me3 modified histone binding +name: H3K9me3 histone reader activity namespace: molecular_function -def: "Binding to a histone H3 in which the lysine residue at position 9 has been modified by trimethylation." [PMID:30110338] -is_a: GO:0035064 ! methylated histone binding +def: "A histone reader that recognizes a histone H3 trimethylated at lysine 9." [PMID:30110338] +synonym: "H3K9me3 modified histone binding" NARROW [] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI created_by: dph creation_date: 2018-09-05T12:58:43Z @@ -450096,6 +450102,57 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2024-11-12T09:29:56Z +[Term] +id: GO:0140002 +name: H3K4me3 histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 trimethylated at lysine 4." [PMID:15647753, PMID:23318260] +synonym: "H3-K4me3 modified histone binding" NARROW [] +synonym: "H3K4me3 modified histone binding" NARROW [] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI +created_by: pg +creation_date: 2024-11-29T14:13:16Z + +[Term] +id: GO:0140003 +name: H3K36me3 histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 trimethylated at lysine 36." [PMID:15489290, PMID:16364921] +synonym: "H3-K36me3 modified histone binding" NARROW [] +synonym: "H3K36me3 modified histone binding" NARROW [] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI +created_by: pg +creation_date: 2024-11-29T14:20:22Z + +[Term] +id: GO:0140004 +name: H3Q5ser histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H3 serotonylated at glutamine 5." [PMID:34144982] +synonym: "H3Q5-serotonin histone reader activity" EXACT [] +synonym: "H3Q5-serotonin modified histone binding" NARROW [] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29337" xsd:anyURI +created_by: pg +creation_date: 2024-11-29T14:37:52Z + +[Term] +id: GO:0140005 +name: H4K20me2 histone reader activity +namespace: molecular_function +def: "A histone reader that recognizes a histone H4 dimethylated at lysine 20." [PMID:22150589] +synonym: "H4K20me2 modified histone binding" NARROW [] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24912" xsd:anyURI +created_by: pg +creation_date: 2024-11-29T15:16:39Z + [Term] id: GO:0140007 name: KICSTOR complex @@ -453960,7 +454017,7 @@ creation_date: 2020-05-06T07:47:09Z id: GO:0140463 name: chromatin-protein adaptor activity namespace: molecular_function -def: "The binding activity of a molecule that brings together a protein or a protein complex with a nucleosome, to establish or maintain the chromatin localization of the protein, or protein complex." [PMID:32277274] +def: "An adaptor activity that brings together a protein and a region of the chromatin, such as a nucleosome, to establish or maintain the chromatin localization of the protein, or the complex to which it belongs." [PMID:32277274] synonym: "chromatin adaptor" EXACT [] synonym: "chromatin adaptor activity" EXACT [] synonym: "chromatin receptor" EXACT [] @@ -454940,7 +454997,7 @@ creation_date: 2020-11-25T16:07:58Z id: GO:0140566 name: histone reader activity namespace: molecular_function -def: "A chromatin adaptor that recognizes specific forms of histones, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176, PMID:34726351] +def: "A chromatin adaptor activity that brings together a protein and a specific form of histone, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176, PMID:34726351] synonym: "epigenetic reader" BROAD [] synonym: "histone reader" EXACT [] is_a: GO:0140463 ! chromatin-protein adaptor activity @@ -584071,10 +584128,13 @@ creation_date: 2015-10-28T22:31:13Z [Term] id: GO:1990889 -name: H4K20me3 modified histone binding +name: H4K20me3 histone reader activity namespace: molecular_function -def: "Binding to a histone H4 in which the lysine residue at position 20 has been modified by trimethylation." [PMID:22150589] -is_a: GO:0035064 ! methylated histone binding +def: "A histone reader that recognizes a histone H4 trimethylated at lysine 20." [PMID:22150589] +synonym: "H4K20me3 modified histone binding" NARROW [] +is_a: GO:0140566 ! histone reader activity +relationship: has_part GO:0035064 ! methylated histone binding +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27427" xsd:anyURI created_by: al creation_date: 2015-10-30T15:43:09Z