Term issue: Histone H3 modifications

[ValWood]

Since:

PMID:19362535

S10 of histone H3 is phosphorylated during mitosis and displaces HP1 proteins (including Swi6) from chromatin (Fischle et al., 2005; Hirota et al., 2005; Yamada et al., 2005). We investigated whether binding of Swi6 and Chp1 to H3K9me peptides was affected by S10 phosphorylation and found a strong reduction in both Chp1- and Swi6-binding affinity (Table S2; Figure S2B),

I think we should make the
hht1 https://proconsortium.org/app/entry/PR:000027578/ + UnP S10 hht2 https://proconsortium.org/app/entry/PR:000027604/ + UnP S10 hht3 https://proconsortium.org/app/entry/PR:000027604/ + UnP S10

and I will use these as the active form for HP1 protein binding

[nataled]

Hi Val, Just so I'm clear... You want the three terms referenced above to be modified so that they include a specifically unphosphorylated S10, or is it that you want three new terms that are basically like the ones referenced, but with the added specification?

[ValWood]

Sorry for the delay, we would need new terms (not modified terms, we still need K3K9-Me)

K3K9-Me + P S10 (for each of the 3 histones H3s) plus the K3K9-Me S10-unP forms (for each of the 3 histones H3s)

and the P S10 (for each of the 3 histones H3s) forms to annotate these older papers "S10 of histone H3 is phosphorylated during mitosis and displaces HP1 proteins (including Swi6) from chromatin (Fischle et al., 2005; Hirota et al., 2005; Yamada et al., 2005)." where the K3K9-Me status won't be known.

It's a slight headmelt at the moment but I will get the community to check the histones code combinations once I have curated most of the key papers.

Does that make sense?

[nataled]

Hi Val, here are your terms. I did make the S10phos-only terms even though it seems like those three cited papers all refer to an acetylated Lys-10 as well (at least based on abstract). Let me know if I should delete the last three.

hht1 + AcLys10 + PhosSer11 = PR:000085726 hht2 + AcLys10 + PhosSer11 = PR:000085727 hht3 + AcLys10 + PhosSer11 = PR:000085728 hht1 + AcLys10 + unPhosSer11 = PR:000085729 hht2 + AcLys10 + unPhosSer11 = PR:000085730 hht3 + AcLys10 + unPhosSer11 = PR:000085731 hht1 + PhosSer11 = PR:000085732 hht2 + PhosSer11 = PR:000085733 hht3 + PhosSer11 = PR:000085734

[Term]
id: PR:000085726
name: histone H3.1, initiator methionine removed K9-methylated and phosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-9 and phosphorylated on Ser-10. Example: UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, MOD:00046." [PRO:DAN, PomBase:VW, PMID:19362535]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue numbers are different because the initial methionine is not counted.
synonym: "Spom-hht1/InitMet-/K9MePhos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-10, MOD:00663|Ser-11, MOD:00046" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, MOD:00046" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027574 ! histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085727
name: histone H3.2, initiator methionine removed K9-methylated and phosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-9 and phosphorylated on Ser-10. Example: UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, MOD:00046." [PRO:DAN, PomBase:VW, PMID:19362535]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue numbers are different because the initial methionine is not counted.
synonym: "Spom-hht2/InitMet-/K9MePhos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-10, MOD:00663|Ser-11, MOD:00046" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, MOD:00046" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027580 ! histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085728
name: histone H3.3, initiator methionine removed K9-methylated and phosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-9 and phosphorylated on Ser-10. UniProtKB:P10651, 2-136, Lys-10, MOD:00663|Ser-11, MOD:00046." [PRO:DAN, PomBase:VW, PMID:19362535]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue numbers are different because the initial methionine is not counted.
synonym: "Spom-hht3/InitMet-/K9MePhos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Lys-10, MOD:00663|Ser-11, MOD:00046" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Lys-10, MOD:00663|Ser-11, MOD:00046" EXACT PRO-proteoform-std [PRO:DNx]
is_a: PR:000027598 ! histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085729
name: histone H3.1, initiator methionine removed K9-methylated and unphosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-9 but not phosphorylated on Ser-10. Example: UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, PR:000026291." [PRO:DAN, PomBase:VW, PMID:19362535]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue numbers are different because the initial methionine is not counted.
synonym: "Spom-hht1/InitMet-/K9MeUnPhos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-10, MOD:00663|Ser-11, PR:000026291" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, PR:000026291" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027574 ! histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085730
name: histone H3.2, initiator methionine removed K9-methylated and unphosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-9 but not phosphorylated on Ser-10. Example: UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, PR:000026291." [PRO:DAN, PomBase:VW, PMID:19362535]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue numbers are different because the initial methionine is not counted.
synonym: "Spom-hht2/InitMet-/K9MeUnPhos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Lys-10, MOD:00663|Ser-11, PR:000026291" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Lys-10, MOD:00663|Ser-11, PR:000026291" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027580 ! histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085731
name: histone H3.3, initiator methionine removed K9-methylated and unphosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe) that has been methylated on Lys-9 but not phosphorylated on Ser-10. UniProtKB:P10651, 2-136, Lys-10, MOD:00663|Ser-11, PR:000026291." [PRO:DAN, PomBase:VW, PMID:19362535]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited residue numbers are different because the initial methionine is not counted.
synonym: "Spom-hht3/InitMet-/K9MeUnPhos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Lys-10, MOD:00663|Ser-11, PR:000026291" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Lys-10, MOD:00663|Ser-11, PR:000026291" EXACT PRO-proteoform-std [PRO:DNx]
is_a: PR:000027598 ! histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: has_part MOD:00663 ! methylated lysine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085732
name: histone H3.1, initiator methionine removed phosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe) that has been phosphorylated on Ser-10. Example: UniProtKB:P09988, 2-136, Ser-11, MOD:00046." [PRO:DAN, PomBase:VW]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue number is different because the initial methionine is not counted.
synonym: "Spom-hht1/InitMet-/Phos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Ser-11, MOD:00046" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Ser-11, MOD:00046" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027574 ! histone H3.1, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085733
name: histone H3.2, initiator methionine removed phosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe) that has been phosphorylated on Ser-10. Example: UniProtKB:P09988, 2-136, Ser-11, MOD:00046." [PRO:DAN, PomBase:VW]
comment: Category=organism-modification. Requested by=PomBase. Note that in the article cited the residue number is different because the initial methionine is not counted.
synonym: "Spom-hht2/InitMet-/Phos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221366, Ser-11, MOD:00046" RELATED PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P09988, 2-136, Ser-11, MOD:00046" RELATED PRO-proteoform-std [PRO:DNx]
is_a: PR:000027580 ! histone H3.2, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe

[Term]
id: PR:000085734
name: histone H3.3, initiator methionine removed phosphorylated 1 (Schizosaccharomyces pombe)
def: "A histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe) that has been phosphorylated on Ser-10. UniProtKB:P10651, 2-136, Ser-11, MOD:00046." [PRO:DAN, PomBase:VW]
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-/Phos:1" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000221367, Ser-11, MOD:00046" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P10651, 2-136, Ser-11, MOD:00046" EXACT PRO-proteoform-std [PRO:DNx]
is_a: PR:000027598 ! histone H3.3, initiator methionine removed form (Schizosaccharomyces pombe)
relationship: has_part MOD:00046 ! O-phospho-L-serine
relationship: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe