request new term: Telomeric D-loops

[NancyCampbell]

I am looking for "telomeric D-loop" on SO. I found a related term SO:0000297 which refers to the same D-loop (as far as the definition goes and at least structurally). Albeit the SO definition only refers to D-loops in the mitochondria and the D-loops I am annotating are in the telomeric DNA at chromosome termini. PMID:10338204, PMID:24012755

I would like to use this in my annotation in GO so would be very useful to have it. I have quite a few annotations to a number of proteins for which telomeric D-loop SO ID would be very handy. It might of interest to mention that a telomeric D-loop related new ontology term was requested from GO which has been approved. Here is the Github link: https://github.com/geneontology/go-ontology/issues/12881# if you can't access the GitHub ticket, this is the resolution: [Term] +id: GO:0061820 +name: telomeric D-loop disassembly +def: "A telomere loop disassembly process that results in the disassembly of telomeric D-loops. A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus." [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:10338204, PMID:24012755] +is_a: GO:0090657 ! telomeric loop disassembly +created_by: dph

[NancyCampbell]

Hi,

Can you please update me on whether there have been any progress with regards to this request. Thanks.

Regards

Nancy

[nicoleruiz]

I have added SO:0002171 telomeric_D_loop as a child of origin_of_replication. The definition is "A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus." I took this from the definition of the GO term you referenced and made a citation in the comment section.

I think we also need to have a term for telomeric_T_loop. Would this term be a sibling of telomeric_D_loop or a child of it?

[NancyCampbell]

Hi,

Great. Thank you. Definition looks great for SO:0002171 telomeric_D_loop. Yes please - adding telomeric-loop would certainly complete the picture. May I clarifiy the following:

Naming: telomeric-loop or t-loop (t stands for telomeric) is more accurate than telomeric_T_loop.

Synonyms: Telomeric-loop could be the main term and t-loop a synonym, if possible!?

Hierarchy: Good question! Well, in early refernces describing these two loops (the year 2000 ish), it was not made clear whether d-loop forms part of t-loop or is a separate adjacent structure. However, more recently (2017), d-loop is shown as part of the t-loop, here is an example from PMID 28183782 figure 1 B:

So it would be:

Telomeric D-loop child_of Telomeric-loop.

Regards

Nancy

[davidwsant]

Hi Nancy,

It looks like the term telomeric_D_loop was created in 2017, but telomeric loop was not created. We have had a change in staff and I am now going through the old issue requests that were not closed.

Here is what I have so far:

id: New name: telomeric_loop def: "The large loop structures at the end of telomeres. Here, the single-stranded DNA curls around in a long circle, stabilized by telomere-binding proteins." References: PMID:17012276, PMID:10338204, PMID:15071557, PMID:24012755 comment: Added in reference to Gene Ontology term telomeric loop formation GO:0031627. synonym: "telomeric loop" synonym: "T loop" is_a: origin_of_replication (SO:0000296)

And this would be accompanied by a change in the relationship of telomeric_D_loop to "is_a telomeric_loop"

Does this sound correct?

Thanks,

Dave

@NancyCampbell