Obsoletion request: DNA methylation & children, as well as their regulation terms

[pgaudet]

Dear all,

The proposal has been made to obsolete DNA methylation & children, as well as their regulation terms:

• GO:0006306 DNA methylation
• GO:0032775 DNA methylation on adenine
• GO:0032776 DNA methylation on cytosine
• GO:0090116 C-5 methylation of cytosine
• GO:0010424 DNA methylation on cytosine within a CG sequence (same as 'GO:0044027 negative regulation of gene expression via chromosomal CpG dinucleotide methylation')
• GO:0010426 DNA methylation on cytosine within a CHH sequence
• GO:0010425 DNA methylation on cytosine within a CNG sequence
• • These two terms represent MFs that can be part of different biological pathways, for example all 3 methylation patterns are possible for RNA-directed DNA methylation, see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923318/
• GO:0090124 N-4 methylation of cytosine
• GO:0044030 regulation of DNA methylation
• GO:1905642 negative regulation of DNA methylation
• GO:1905643 positive regulation of DNA methylation

The reason for obsoletion is that these represent molecular functions. Consider:

GO:0009008 DNA-methyltransferase activity GO:0003886 DNA (cytosine-5-)-methyltransferase activity GO:0051718 DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates GO:0051719 DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates GO:0051720 DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates' GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity GO:0015667 site-specific DNA-methyltransferase (cytosine-N4-specific) activity GO:0120328 ATP-dependent DNA (cytosine-5-)-methyltransferase activity

For BP, consider 'GO:0040029 epigenetic regulation of gene expression' or a child.

Annotations are here: https://github.com/geneontology/go-annotation/issues/4729 Regulation: https://github.com/geneontology/go-annotation/issues/4945

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

I'd like to proceed with the obsoletion on December 22nd, 2023.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/26602

Thanks, Pascale

[pgaudet]

Hi everyone,

Since some new GO terms are not yet available, I will postpone the obsoletion.

Note that I have also made a new ticket for direct annotations to DNA methylation: https://github.com/geneontology/go-annotation/issues/4872

Thanks, Pascale

[pgaudet]

• GO:0006305 DNA alkylation: no annotations, no mappings GO:0006306 DNA methylation: no annotations, no mappings

[pgaudet]

Still need to obsolete GO:0044030 regulation of DNA methylation Giving people some more time to fix annotations. Now aim for Feb 1, 2024