gocentral
commented
10 years ago Hi Ingrid,
The PMIDs supporting GO:0010385 and GO:0044729 do indeed refer to cytosine, but I think it would be ok to expand these terms to include binding to other methylated residues (there is no reference in these term names, nor any synonym, that implies a specificity for cytosine only; methyl-cytosine happens to be detected more frequently than adenine). There is a lot of residue-specific information in the branch under 'DNA methylation', but that's a different issue and it warrants more granularity (also there are only 17 manual experimental annotations to GO:0010385, and 2 to GO:0044729, as compared to 407 for 'DNA methylation' and children). I left the term names as they are, and changed "Cytosine methylation in DNA" in the defs with "Methylation of cytosine or adenine in DNA".
Thanks, Paola
Original comment by: paolaroncaglia
The definition of the terms are currently "Interacting selectively and non-covalently with double-stranded methylated DNA. Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks." and "Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Cytosine methylation in DNA is an important mechanism for establishing stable heritable epigenetic marks.", respectively. I am wondering whether inclusion of the cytosine methylation language in the definition is meant to restrict usage to proteins that bind cytosine-methylated DNA. I did annotate the E. coli SeqA protein to these terms, but SeqA binds DNA with methylated and hemimethylated A residues.
Should the term definitions be changed, clarified, new terms created, and/or should I not annotate SeqA to these terms? I'm not sure.
Thanks, Ingrid
Reported by: imk07
Original Ticket: geneontology/ontology-requests/10933