Review annotations to some DNA methylation terms on specific residues

[pgaudet]

GO:0090116 | C-5 methylation of cytosine GO:0032775 | DNA methylation on adenine GO:0010424 | DNA methylation on cytosine within a CG sequence GO:0010426 | DNA methylation on cytosine within a CHH sequence GO:0010425 | DNA methylation on cytosine within a CNG sequence GO:0032776 | DNA methylation on cytosine GO:0090124 | N-4 methylation of cytosine

Annotations are here: https://docs.google.com/spreadsheets/d/1GvBHn8ISJJcs5aY716S9_rtv6k-qvT0iE03_0MNSJHc/edit#gid=0

Annotations to regulation terms are here: https://docs.google.com/spreadsheets/d/1vIoh1iIGFg22FdZto1BYHv7UZIuMqzB2N_U-rdbSXFw/edit#gid=0

ARUK-UCL 1 (done) BHF-UCL 6 (done) ComplexPortal 8 EcoCyc 3 MGI 15 ParkinsonsUK-UCL 1 (done) RGD 11 TAIR 22 ZFIN 15 InterPro: 6

[pgaudet]

• [x] InterPro:IPR008593 DNA N-6-adenine-methyltransferase > GO:DNA methylation on adenine ; GO:0032775 >> change to DNA restriction-modification system
• [x] InterPro:IPR012186 Adenine modification methylase, M.StsI-type > GO:DNA methylation on adenine ; GO:0032775 >> change to DNA restriction-modification system
• [x] InterPro:IPR012263 Adenine modification methylase, M.EcoRV-type > GO:DNA methylation on adenine ; GO:0032775 >> change to DNA restriction-modification system
• [x] InterPro:IPR012327 D12 class N6 adenine-specific DNA methyltransferase > GO:DNA methylation on adenine ; GO:0032775 >> change to DNA restriction-modification system
• [x] InterPro:IPR017127 Ribosomal protein uL3 glutamine methyltransferase > GO:DNA methylation on adenine ; GO:0032775 >> according to the InterPro description, this is a protein methylase
• [x] InterPro:IPR017198 DNA (cytosine-5)-methyltransferase 1-like > GO:C-5 methylation of cytosine ; GO:0090116
• [x] InterPro:IPR017985 DNA methylase, N-4 cytosine-specific, conserved site > GO:N-4 methylation of cytosine ; GO:0090124 >> change to DNA restriction-modification system

[amandamackie]

EcoCyc done

[blazaropinto]

Thank you for this, all the mentioned entries are updated. Thank you so much for pointing out the case of IPR017127, it is indeed representing a protein methyltransferase and not a DNA one, I updated the GO terms. Also in IPR017198 I updated BP to GO:0010424: DNA methylation on cytosine within a CG sequence. Best, Beatriz

[LiNiMGI]

Hi @pgaudet, The excel sheet does not include annotations to GO:0006306 DNA methylation. Is there a separate list for annotations to GO:0006306 DNA methylation? according to go-announcements/issues/637, GO:0006306 DNA methylation will also be obsoleted. Thanks, Li

[pgaudet]

Hi @LiNiMGI there are two spreadsheets:

Methylation: https://docs.google.com/spreadsheets/d/1GvBHn8ISJJcs5aY716S9_rtv6k-qvT0iE03_0MNSJHc/edit#gid=0

Regulation of methylation: https://docs.google.com/spreadsheets/d/1vIoh1iIGFg22FdZto1BYHv7UZIuMqzB2N_U-rdbSXFw/edit#gid=0

[sandraorchard]

Complex Portal done

[LiNiMGI]

Hi @pgaudet, I found none of the spreadsheets include existing annotations to the GO term "GO:0006306 DNA methylation", thanks.

[pgaudet]

Hi @LiNiMGI

I will do a separate spreadsheet for DNA methylation, thanks for the reminder!

[sramachand]

ZFIN done

[pgaudet]

thanks @blazaropinto

Sorry I skipped one entry - IPR017198 should be moved to DNA methylation-dependent heterochromatin formation; GO:0010424: DNA methylation on cytosine within a CG sequence. will also be obsoleted.

Thanks, Pascale

[pgaudet]

According to the spreadseet, there are still annotations by MGI @LiNiMGI RGD @gthayman and TAIR @tberardini

[blazaropinto]

Hi Pascale,

Thank you for this. That's updated now. The changes will be available in the next InterPro release.

Best,

Beatriz

[gthayman]

RGD done.

[LiNiMGI]

MGI done.

[pgaudet]

Obsoletion done. Remaining annotations will appear in error reports.