H3 K9me3
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Currently in PRO we have the following term (at bottom), which appears to be identical to what you are requesting except for two things:
1) The methylation type (mono-, di-, or tri-) is not indicated;
2) Removal of an initiator methionine is indicated.
I can very quickly create a new term based on that old one (with the specific methylation type indicated), but I just need to know about the initiator methionine removal. Do you wish to have the new term have that removed, or not?
Considering the definition, it is also possible that the old term should be revised to reflect the more-specific methylation type.
[Term]
id: PR:000027604
name: histone H3.3, initiator methionine removed K9-methylated form (Schizosaccharomyces pombe)
def: "A fungal histone H3.3, initiator methionine removed methylated form that is recognized by the HP1-like protein Swi6 in Schizosaccharomyces pombe. UniProtKB:P10651, 2-136, Lys-10, MOD:00663." [PRO:DAN, PomBase:MAH, PMID:11242054]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue number is different because the initial methionine is not counted.
synonym: "Spom-hht3/InitMet-/K9me" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Lys-10, MOD:00663" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Lys-10, MOD:00663" EXACT PRO-proteoform-std [PRO:DNx]
is_a: PR:000027603 ! fungal histone H3.3, initiator methionine removed methylated form
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
Hi Darren,
yes please methionine removal is fine. I think this should be the defult on all of our moified histnes since the 'active' form is demethylated?
Val
It turns out we already have the requested term! It is PR:000044705 (reproduced below). I added your additional evidence.
In fact, we have K9 methylation terms for pombe H3.1, H3.2, and H3.3, and for each methylation type: non-specific, mono-, di-, and trimethylated. Sorry I didn't catch it earlier.
[Term]
id: PR:000044705
name: histone H3.3, initiator methionine removed K9-trimethylated form (Schizosaccharomyces pombe)
def: "A histone H3.3, initiator methionine removed K9-methylated form (Schizosaccharomyces pombe) whose methylation type is trimethylation. UniProtKB:P10651, 2-136, Lys-10, MOD:00083." [PRO:DAN, PomBase:VW, PMID:23849629, PMID:30110338]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue number is different because the initial methionine is not counted.
synonym: "Spom-hht3/InitMet-/K9Me3" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Lys-10, MOD:00083" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Lys-10, MOD:00083" EXACT PRO-proteoform-std [PRO:DNx]
intersection_of: PR:000027604 ! histone H3.3, initiator methionine removed K9-methylated form (Schizosaccharomyces pombe)
intersection_of: has_part MOD:00083 ! N6,N6,N6-trimethyl-L-lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe
my fault, I always forget where I can search, so I just searched in teh SF tracker.
Can you remind me where I should search ?
v
It just occurred to me that I might have mis-interpreted your request. Did you want a term that covers K9-trimethylation for any of the H3 types? We have terms that cover each of the specific types (H3.1, H3.2, H3.3) but not one that covers (H3.1 or H3.2 or H3.3).
All three is fine. We can't distinguish as they are identical, and I wnat the annotation to appear as
modification on all 3 objects.
v
Okay, in that case, for K9 trimethylation, you want the following:
hht1 PR:000044699
hht2 PR:000044702
hht3 PR:000044705
To search, you can go to the PRO main page https://proconsortium.org/pro/pro.shtml and use either the search or the SPARQL (with examples that cover the request you(?) made once upon a time on how to find all PRO entries for a specific gene). The SF tracker won't always have everything because sometimes I anticipate future needs ;)