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Source ontology files for the Gene Ontology
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NTR: [MF terms missing for BPs pending obsoletion, histone modifications] #22769

Closed ValWood closed 1 year ago

ValWood commented 2 years ago

to replace BP GO:0016578 histone deubiquitination. Definition: An isopeptidase activity that cleaves ubiquitin from a histone to which it is conjugated. Parent: GO:0101005 deubiquitinase activity Ref: PMID:16611979 PMID:29352077 Related synonym: histone deubiquitination

I don't know if we want/need terms specific for di/tri methylation as I am not sure if different enzymes perform these modifications, or that if a methyl transfer are can do is methylation it can also do trimethylation Maybe we should consult Rhea about this?

pgaudet commented 2 years ago

I don't know if we want/need terms specific for di/tri methylation as I am not sure if different enzymes perform these modifications, or that if a methyl transfer are can do is methylation it can also do trimethylation

@sjm41 and I looked at that in detail here #21089

Some enzymes do more than one methylation, some do a single one. We tried to represent all known activities.

krchristie commented 2 years ago

I don't know if we want/need terms specific for di/tri methylation as I am not sure if different enzymes perform these modifications, or that if a methyl transfer are can do is methylation it can also do trimethylation

@sjm41 and I looked at that in detail here #21089

Some enzymes do more than one methylation, some do a single one. We tried to represent all known activities.

I am trying to reannotate Kmt2b (aka Mll2) from this paper:

Andreu-Vieyra CV, et al. 2010. MLL2 is required in oocytes for bulk histone 3 lysine 4 trimethylation and transcriptional silencing. PLoS Biol. 2010 Aug 17;8(8):e1000453. doi:10.1371/journal.pbio.1000453. PMID:20808952

It says that Kmt2b does the H3K4 dimethylation and trimethylation, which can not be done by other histone methylases in the absence of Kmt2b, and also that absence of Kmt2b does not affect H3K4 monomethylation, which appears to be done by another enzyme or enzymes. Thus, I need the individually broken out MF terms to replace these three BP terms:

Also please make sure that all of these terms have both the dash-containing and dashless versions of the histone site specificity, e.g. H3-K4 and H3K4. I was having problems finding all the terms related to H3-K4 modification in Protege because of inconsistency in the usage versus absence of the dash in these terms

ValWood commented 1 year ago

Can we get NTR: histone deubiquitinase activity from this ticket (then GO:0016578 histone deubiquitination can be obsoleted)

ValWood commented 1 year ago

Can we get NTR: histone deubiquitinase activity from this ticket (then GO:0016578 histone deubiquitination can be obsoleted)

pgaudet commented 1 year ago

@ValWood , for

NTR: histone H4K12 deacetylase activity to replace BP GO:1990679 histone H4-K12 deacetylation Definition: Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 12) + H2O = histone H4 L-lysine (position12) + acetate. This reaction represents the removal of an acetyl group from lysine at position 12 of the histone H4 protein. Parent: GO:0004407 histone deacetylase activity Ref: PMID:22771823 Related synonym: histone H4-K12 deacetylation

I cannot find evidence for this activity in the paper - can you please double check?

pgaudet commented 1 year ago

+[Term] +id: GO:0140934 +name: histone deubiquitinase activity +namespace: molecular_function +def: "A deubiquitinase that cleaves ubiquitin from a histone protein to which it is conjugated." [PMID:18226187] +synonym: "histone deubiquitination" RELATED [] +is_a: GO:0101005 ! deubiquitinase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22769 xsd:anyURI +created_by: pg +creation_date: 2022-11-01T07:39:52Z + +[Term] +id: GO:0140935 +name: histone H2B conserved C-terminal lysine deubiquitinase activity +namespace: molecular_function +def: "A histone deubiquitinase that cleaves ubiquitin from the conserved C-terminal lysine residue of a histone H2B protein to which it is conjugated. The conserved lysine residue is K119 in fission yeast, K123 in budding yeast, and K120 in mammals." [] +synonym: "histone conserved C-terminal lysine deubiquitination" RELATED [] +is_a: GO:0140936 ! histone H2B deubiquitinase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22769 xsd:anyURI +created_by: pg +creation_date: 2022-11-01T07:46:50Z + +[Term] +id: GO:0140936 +name: histone H2B deubiquitinase activity +namespace: molecular_function +def: "A histone deubiquitinase that cleaves ubiquitin from a histone H2B protein to which it is conjugated." [] +synonym: "histone H2B deubiquitination" RELATED [] +is_a: GO:0140934 ! histone deubiquitinase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22769 xsd:anyURI +created_by: pg +creation_date: 2022-11-01T08:10:30Z

+[Term] +id: GO:0140937 +name: histone H4K12 deacetylase activity +namespace: molecular_function +def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 12) + H2O = histone H4 L-lysine (position 12) + acetate. This reaction represents the removal of an acetyl group from lysine at position 12 of the histone H4 protein." [GOC:vw, PMID:15293224] +synonym: "histone deacetylase activity (H4-K12 specific)" EXACT [] +synonym: "histone H4-K12 deacetylase activity" EXACT [] +synonym: "histone H4-K12 deacetylation" RELATED [] +is_a: GO:0004407 ! histone deacetylase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22769 xsd:anyURI +created_by: pg +creation_date: 2022-11-01T08:12:49Z

pgaudet commented 1 year ago

+[Term] +id: GO:0140950 +name: histone H2A deubiquitinase activity +namespace: molecular_function +def: "A histone deubiquitinase that cleaves ubiquitin from a histone H2A protein to which it is conjugated." [PMID:18226187, PMID:20436459] +synonym: "histone H2A deubiquitination" RELATED [] +is_a: GO:0140934 ! histone deubiquitinase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22769 xsd:anyURI +created_by: pg +creation_date: 2022-11-01T11:11:26Z

ValWood commented 1 year ago

for NTR: histone H4K12 deacetylase activity use PMID: 15293224

pgaudet commented 1 year ago

+[Term] +id: GO:0140954 +name: histone H3K36 mono/dimethyltransferase activity +namespace: molecular_function +def: "Catalysis of the reaction: L-lysyl36-[histone H3] + 2 S-adenosyl-L-methionine = 2 H+ + N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 S-adenosyl-L-homocysteine. This reaction is the successive addition of two methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me2." [RHEA:60308] +synonym: "histone H3K27 mono/dimethylase activity" EXACT [] +xref: EC:2.1.1.357 +xref: RHEA:60308 +is_a: GO:0046975 ! histone H3K36 methyltransferase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22588 xsd:anyURI +created_by: pg +creation_date: 2022-11-01T15:06:50Z + +[Term] +id: GO:0140955 +name: histone H3K36 mono/di/trimethyltransferase activity +namespace: molecular_function +def: "Catalysis of the reaction: L-lysyl36-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of three methyl groups to the lysine residue at position 36 of histone H3, producing histone H3K36me3." [RHEA:60324] +synonym: "histone H3K27 mono/dimethylase activity" EXACT [] +xref: EC:2.1.1.359 +xref: RHEA:60324 +is_a: GO:0046975 ! histone H3K36 methyltransferase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22588 xsd:anyURI +created_by: pg +creation_date: 2022-11-01T15:18:59Z + +[Term] +id: GO:0140956 +name: histone H3K79 trimethyltransferase activity +namespace: molecular_function +def: "Catalysis of the reaction: L-lysyl79-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl79-[histone H3] + 3 S-adenosyl-L-homocysteine. This reaction is the successive addition of up to three methyl group to the lysine residue at position 79 of the histone H3 protein, producing H3K79me3." [PMID:15371351, RHEA:60328] +synonym: "histone H3K79 trimethylase activity" EXACT [] +synonym: "histone lysine N-trimethyltransferase activity (H3-K79 specific)" EXACT [] +synonym: "histone trimethylase activity (H3-K79 specific)" EXACT [GOC:mah] +synonym: "histone trimethyltransferase activity (H3-K79 specific)" EXACT [] +synonym: "histone-H3K79 trimethyltransferase activity" EXACT [] +xref: EC:2.1.1.360 +xref: RHEA:60328 +is_a: GO:0031151 ! histone H3K79 methyltransferase activity +created_by: pg +creation_date: 2022-11-01T15:47:14Z

pgaudet commented 1 year ago

Still need to find evidence for this term:

[Term] id: GO:0140935 name: histone H2B conserved C-terminal lysine deubiquitinase activity namespace: molecular_function def: "A histone deubiquitinase that cleaves ubiquitin from the conserved C-terminal lysine residue of a histone H2B protein to which it is conjugated. The conserved lysine residue is K119 in fission yeast, K123 in budding yeast, and K120 in mammals." [] synonym: "histone conserved C-terminal lysine deubiquitination" RELATED [] is_a: GO:0140936 ! histone H2B deubiquitinase activity property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22769 xsd:anyURI created_by: pg creation_date: 2022-11-01T07:46:50Z

ValWood commented 1 year ago

see https://www.ebi.ac.uk/QuickGO/term/GO:0035616 for GO:0140935 (its Ubp8 SAGA complex ubiquitin C-terminal hydrolase Ubp8)