NTR: histone H1 demethylase activity

[pgaudet]

Please provide as much information as you can:

• Suggested term label:
  histone H1 demethylase activity

• Definition (free text)
  Catalysis of the removal of a methyl group from a modified lysine residue of the histone H1 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.

• Reference, in format PMID:#######
  PMID:19144645

• Gene product name and ID to be annotated to this term
  O94953 · KDM4B_HUMAN

• Parent term(s)
  histone demethylase activity

• Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED)

• Cross-references
  NA

• Any other information

[raymond91125]

+[Term]
+id: GO:0160243
+name: histone H1 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a modified lysine residue of the histone H1 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:19144645]
+is_a: GO:0032452 ! histone demethylase activity
+property_value: term_tracker_item "#29636" xsd:anyURI
+created_by: rynl
+creation_date: 2025-01-31T21:51:52Z

[raymond91125]

Should we submit a request for a RHEA?

[pgaudet]

I think RHEA only creates reactions if there is a specific residue ?
See https://www.rhea-db.org/rhea?query=histone+demethylase+activity

@amorgat @kaxelsen Is this correct?

[raymond91125]

I thought we are trying to avoid having leaf terms of catalytic activities without EC or RHEA xref. #28340.

[pgaudet]

Yes, we do try ! But it doesn't always work.

After discussion with @colinlog , we decided that there were too many lysine residues in histone H1 to capture them all in GO (see also https://www.uniprot.org/uniprotkb/P07305/entry#sequences)

[kaxelsen]

I think RHEA only creates reactions if there is a specific residue ? See https://www.rhea-db.org/rhea?query=histone+demethylase+activity

@amorgat @kaxelsen Is this correct?

@pgaudet There are no strict rules for this. We do create specific reactions in some cases, mostly if there is an enzyme specific for a specific position and/or if there is a specific EC number. The problem adding specific positions is that very often the position number is not the same in different species, and then the reaction becomes species specific, and that is too narrow for Rhea.

[pgaudet]

If that's the case, they we would love to have RHEA reactions for the following histone demethylases:

GO:0160243 histone H1 demethylase activity

GO:0141052 histone H3 demethylase activity

GO:0051864 histone H3K36 demethylase activity
GO:0071558 histone H3K27me2/H3K27me3 demethylase activity
GO:0140760 histone H3K56me2/H3K56me3 demethylase activity
GO:0032453 histone H3K4 demethylase activity
GO:0032454 histone H3K9 demethylase activity
GO:0033746 histone H3R2 demethylase activity

GO:0141058 histone H4 demethylase activity
GO:0033749 histone H4R3 demethylase activity
GO:0035575 histone H4K20 demethylase activity

As far as I know, these are all 2-oxoglutarate-dependent dioxygenase activity

Thanks, Pascale