dsDNA loop formation is_a chromatin remodelling?

[Antonialock]

dsDNA loop formation (The formation and maintenance of DNA loops that juxtapose separated regions on the same dsDNA molecule)
is_a chromosome organization

but should it be is_a chromatin remodelling? (Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.)

all annotations to this term are for eukaryotes

[ValWood]

I'm not sure that it should. I think it might depend on which type of DNA loops (chromatin loops yes during packaging yes, but are there other types?). Maybe the term is a bit vague?

[Antonialock]

Promoter-enhancer looping is also chromatin remodelling?

I don’t know much about dna loops...are there other types?

[ValWood]

Ok yes I want really think of any ds ones that aren't....

[Antonialock]

So it looks like prokaryotes also loop their DNA...https://jb.asm.org/content/195/6/1109

if all eukaryotic dsDNA looping is chromatin remodelling though it would be nice if this was reflected in the parentage?

(I actually annotated to Promoter-enhancer looping....I'd be happy if just this term had the chromatin remodelling parent if we're not sure about all dsDNA loops)

[ukemi]

But presumably this term is meant to cover both eukaryotes and prokaryotes. That's probably why it didn't have the chromatin parent.

[Antonialock]

So what's the best thing to do here? co-annotating to chromatin remodelling seems a bit clunky?

[ukemi]

Other than creating a term that encompasses both, co-annotation is the option that I would suggest.

[ValWood]

You could request chromatin looping ;) more precise. But is "looping" an activity, or a process?

[Antonialock]

I think process. I don't know how it works in "all cases" but in the example I looked at the process went something like this

• TF-X binds promoter 1
• Starvation signal to transcribe the gene
• TF-Y binds promoter 2, and nucleosome eviction between promoter 1 and 2
• DNA loop formed between promoter 1 and 2
• gene transcribed

[Antonialock]

(there were some other players involved, that's just broadly how it went from memory)

[Antonialock]

cheers I will request chromatin looping