NTR:homologous recombination

[gocentral]

While doing QC work, we noticed that there are many terms in BP that refer to homologous recombination, but there is no homologous recombination process in and of itself. Should we have 'homologous recombination' as a biological process?

David

Reported by: ukemi

Original Ticket: geneontology/ontology-requests/7313

[gocentral]

David,

it was my understanding that this was covered by GO:0000724: double-strand break repair via homologous recombination

?? Pascale

Original comment by: pgaudet

[gocentral]

That is my understanding too. Will check with Eurie who is the resident recombination expert. Val

Original comment by: ValWood

[gocentral]

Is there homologous recombination outside of ds break repair? If not, we can add 'homologous recombination' as an exact synonym for GO:0000724 (DSB repair via homologous recombination).

This question arose from our looking at:

http://amigo.berkeleybop.org/cgi-bin/amigo/term-details.cgi?term=GO:0001311

The term string 'formation of extrachromosomal circular rDNA by homologous recombination during replicative cell aging' refers to homologous recombination but there's no mention of it in the definition nor is there a link to dsb repair via homologous recombination. Should there be a link?

I will also email Jodi H for her opinion as her dbxref is on this term. I will ask her to comment on this item.

Thanks.

Original comment by: tberardini

[gocentral]

I thought we had a previous conversation about this but can't seem to find the SF item.

'homologous recombination' is a very general term that if often used to represent many different processes - including meiotic recombination, DSBR via homologous recombination, telomere maintenance, etc. Therefore, the catch with adding this as a synonym for 'dsbr via homologous recombination' (GO:0000724) is is that it could lead to misleading annotations.

I'm looking at the entire branch [DNA recombination (GO:0006310) and child terms] to see if homologous recombination can be made a synonym of any of these terms but I'm feeling hesitant about it.

For the specific term 'formation of extrachromosomal circular rDNA by homologous recombination during replicative cell aging', could it be a child of 'recombination within rDNA repeats' (GO:0045458)? I don't know if there will be conflicts with that term mapping up to 'GO:0006308 : DNA catabolic process' and 'DNA metabolic process'.

Original comment by: eurie

[gocentral]

Thanks, Eurie, for looking at this.

Ok, got it. We won't add homologous recombination as an exact synonym of DSBR via HR. That term already has "homologous recombinational repair" as an exact synonym. That's probably ok.

I like the suggested parent 'recombination within rDNA repeats' (GO:0045458). I don't see the conflict for the DNA catabolic process vs. DNA metabolic process though. Perhaps that has changed just recently?

Link to AMIGO graphical view, shortened:

http://bit.ly/deekl4

Original comment by: tberardini

[gocentral]

This might be a silly question, but why isn't it a grouping term dfor all of the terms which are HR?

Val

Original comment by: ValWood

[gocentral]

Because of the BP terms as currently written could be non-homologous. 'mitotic recombination' could be a non-homologous process to end up exchanging genetic material.

Definitely we could re-group but we'd have to review all annotations.

Original comment by: eurie

[gocentral]

I'd be in favor of not reviewing all annotations. :)

I'm happy with the new parent that Eurie has suggested to tie the term in question to recombination. If there are no objections to that, I think we can make that the action item of this SF issue and end there.

Original comment by: tberardini

[gocentral]

found the old SF item: https://sourceforge.net/tracker/?func=detail&aid=1490197&group\_id=36855&atid=440764

Original comment by: mah11

[gocentral]

See wiki page:

http://wiki.geneontology.org/index.php/Recombination\_and\_DNA\_repair

Original comment by: jl242

[gocentral]

• labels: 390929 --> recombination

Original comment by: jl242

[gocentral]

• status: open --> open-later

Original comment by: rebeccafoulger

[gocentral]

Hello all,

I'm assigning this to Tanya as she had worked/commented on this. I'd agree with her most recent comment on this:

> I'm happy with the new parent that Eurie has suggested to tie the term in question to recombination. If there are no objections to that, I think we can make that the action item of this SF issue and end there.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> tairtb

Original comment by: paolaroncaglia

[gocentral]

Added this link as suggested initially by Eurie.

+is_a: GO:0045458 ! recombination within rDNA repeats

Closing.

Original comment by: tberardini

[gocentral]

• status: open-later --> closed-fixed

Original comment by: tberardini