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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: histone H2B conserved C-terminal lysine ubiquitin ligase activity #22138

Closed ValWood closed 2 years ago

ValWood commented 3 years ago

As the modifications will move from BP to MF, I need an MF term to describe the activity corresponding to this process:

GO:0071894 histone H2B conserved C-terminal lysine ubiquitination Definition A histone ubiquitination process in which a ubiquitin monomer is added to a conserved lysine residue in the C-terminus of histone H2B. The conserved lysine residue is K119 in fission yeast, K123 in budding yeast, or K120 in mammals.

histone H2B conserved C-terminal lysine ubiquitin ligase standard def, here is one reference PMID:17363370

pgaudet commented 2 years ago

We need to review annotations - I dont see any ubi ligase annotated, so we need to decide where to rehouse the existing annotations https://docs.google.com/spreadsheets/d/1RWOBUXZSc8FUmASFsBQ03XE1k73Wm9ypFmiB4ivsVgQ/edit#gid=0

ValWood commented 2 years ago

Quite a lot of these are ligases that will go to the new MF term. DTX3L, ring finger protein 8, E3 ubiquitin-protein ligase BRE1A &B,ring finger protein 40 (and the associated conjugating enzymes). Others entities are scaffolds for these complexes.

Some annotations appear to be indirect phenotypes, and most likely already have appropriate annotation to describe a role in heterochromatin assembly or similar..... The process therm that I used which probably applies to most of these is GO:0048096 (chromatin-mediated maintenance of transcription) which was recently renamed to GO:0045815 epigenetic maintenance of chromatin in transcription-competent conformation

this process correlate with increased RNA polymerase II levels at repeat elements embedded within heterochromatin domains causing heterochromatic derepression.

@colinlog is this the correct process for this modification?

colinlog commented 2 years ago

sorry, yes @ValWood , I agree, antagonising heterochromatin leads to euchromatin in this case and that is GO:0045815 epigenetic maintenance of chromatin in transcription-competent conformation. I save my ramble for the next heterochromatin TXN call.

ValWood commented 2 years ago

So what is the term that should be used? All of my annotations to this term must be wrong. I thought I checked these to the revised term but they must have been incorrect to begin with, or, the term has changed in meaning?

This is what I have currently: https://www.pombase.org/results/from/id/50f32fbc-85ec-4bbe-82cc-8c7c4e62b96f Is it just HULC that need to move?

colinlog commented 2 years ago

That list if very fine! All promoter activities. We will add many more.

ValWood commented 2 years ago

OK I thought you were saying I had the wrong term here! OK! Let me know which other complexes should definitely be annotated to this term. I can compile the list of complex->process and check it with the Term Matrix.

ValWood commented 2 years ago

Can we add these? Once we have the MFs we can move the existing BP annotations. Not so many.

pgaudet commented 2 years ago

Thanks for the reminder

+[Term] +id: GO:0140850 +name: histone ubiquitin ligase activity (H2B-K120 specific) +namespace: molecular_function +def: "Catalysis of the transfer of a ubiquitin molecule to histone 2B at the conserved C-terminal lysine (K) residue. The last K residue is at position 119 in fission yeast, 123 in budding yeast, and 120 in mammals." [PMID:17363370] +synonym: "histone H2B conserved C-terminal lysine ubiquitin ligase activity" EXACT [] +is_a: GO:0061630 ! ubiquitin protein ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-13T09:32:28Z

I added the position of the mammalian H2B to be consistent with other activities - OK ?

Thanks, Pascale

pgaudet commented 2 years ago

NTR: histone ubiquitin ligase activity (H3-K14 specific) def: "Catalysis of the transfer of a ubiquitin molecule to histone 3 at the lysine-14 residue. PMID:34010645 PMID:31468675

pgaudet commented 2 years ago

Grouping term: +[Term] +id: GO:0140852 +name: histone ubiquitin ligase activity +namespace: molecular_function +def: "Catalysis of the transfer of ubiquitin to a histone substrate." [GOC:curators] +is_a: GO:0061630 ! ubiquitin protein ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-13T10:38:05Z

+id: GO:0140851 +name: histone ubiquitin ligase activity (H3-K14 specific) +namespace: molecular_function +def: "Catalysis of the transfer of a ubiquitin molecule to histone 3 at the lysine-14 residue." [PMID:31468675, PMID:34010645] +is_a: GO:0140852 ! histone ubiquitin ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-13T10:34:13Z +

pgaudet commented 2 years ago
pgaudet commented 2 years ago

+[Term] +id: GO:0140856 +name: histone ubiquitin ligase activity (H2A-K13 specific) +def: Catalysis of the transfer of a ubiquitin molecule to histone 2 at the lysine-13 residue. {xref="PMID:22980979"} +namespace: molecular_function +is_a: GO:0140852 ! histone ubiquitin ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-20T12:45:05Z +

+[Term] +id: GO:0140858 +name: histone ubiquitin ligase activity (H2A-K15 specific) +def: Catalysis of the transfer of a ubiquitin molecule to histone 2 at the lysine-15 residue. {xref="PMID:22980979"} +namespace: molecular_function +is_a: GO:0140852 ! histone ubiquitin ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-20T12:45:05Z

pgaudet commented 2 years ago

+[Term] +id: GO:0140862 +name: histone ubiquitin ligase activity (H2A-K119 specific) +namespace: molecular_function +def: "Catalysis of the transfer of a ubiquitin molecule to histone 2 at the lysine-119 residue." [PMID:22844243, PMID:25470042] +is_a: GO:0140852 ! histone ubiquitin ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-20T12:45:05Z

ValWood commented 2 years ago

I believe this is the same as https://www.ebi.ac.uk/QuickGO/term/GO:0140850

(check the def) Perhaps it is clearer to call it histone H2B conserved C-terminal lysine ubiquitin ligase activity

We need to know if there are other numbering variations, maybe they are only at the end I am not surer. It also depends if people have used the convention of counting with he methionine removed.

ValWood commented 2 years ago

edited above to correct

pgaudet commented 2 years ago

+[Term] +id: GO:0140862 +name: histone ubiquitin ligase activity (H2A-K119 specific) +namespace: molecular_function +def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-119 residue." [PMID:22844243, PMID:25470042, PMID:28624371] +is_a: GO:0140852 ! histone ubiquitin ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-20T12:45:05Z + +[Term] +id: GO:0140863 +name: histone ubiquitin ligase activity (H2A-K127 specific) +namespace: molecular_function +def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-127 residue." [PMID:28624371] +is_a: GO:0140852 ! histone ubiquitin ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-20T12:45:05Z + +[Term] +id: GO:0140864 +name: histone ubiquitin ligase activity (H2A-K129 specific) +namespace: molecular_function +def: "Catalysis of the transfer of a ubiquitin molecule to histone 2A at the lysine-129 residue." [PMID:28624371] +is_a: GO:0140852 ! histone ubiquitin ligase activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/22138 xsd:anyURI +created_by: pg +creation_date: 2022-06-21T12:12:21Z

pgaudet commented 2 years ago

@ValWood

I believe this is the same as https://www.ebi.ac.uk/QuickGO/term/GO:0140850

It's H2B versus H2A... a bit confusing indeed

ValWood commented 2 years ago

right! should the same naming convention be used, or is 2b more conserved in. numbering?