#50 nucleotide excision repair phenotype
suggested term names:
DNA repair phenotype (GO:0006281 ! DNA repair - def. copied below)
nucleotide excision repair phenotype (GO:0006289 ! nucleotide-excision repair - def. copied below)
increased nucleotide excision repair phenotype
decreased nucleotide excision repair phenotype
Marcus, I'm not sure where these would go in the ontology. I was thinking it would go under 'response to stimulus phenotype' because these enzymes repair DNA lesions caused by UV light and DNA-damaging chemicals. But lesions are also caused by chemicals that are produced endogenously, for example reactive oxygen species. Would that also be response to stimulus? Debby
Definitions:
GO:0006281 ! DNA repair def: "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486]
GO:0006289 ! nucleotide-excision repair def: "A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts)." [PMID:10197977]
comment: Note that although intrastrand cross-link repair is not exactly synonymous with nucleotide excision repair, nucleotide excision repair includes the repair of intrastrand cross-links. The synonym field is being used to reflect the broad substrate specificity of nucleotide excision repair.
Will, Jonathan, Jim, and I discussed whether to add this term to the ontology and decided that, at least for now, it is too granular. Defects in nucleotide excision repair would lead to phenotypes such as decreased UV resistance or increased mutation frequency, and there are terms for such phenotypes in the ontology. To tell whether the observable phenotype was due to defective nucleotide excision repair would require biochemical assays of cell extracts. I recommend that we close this ticket with a 'won't fix' label.