GO:0097521 ; centromere complex, info required

[gocentral]

GO:0097521 ; centromere complex cellular_component A complex composed of proteins and centromeric DNA molecules.

Could we have some more details about this (why it is required?) How does it differ from the kinetochore? thanks

val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/10455

[gocentral]

• assigned_to: Paola Roncaglia

Original comment by: paolaroncaglia

[gocentral]

Hi Val,

This is one of a bunch of component terms that I added as they were needed to create logical definitions for assembly/disassembly terms. So this one stems from:

id: GO:0034508 name: centromere complex assembly def: "The aggregation, arrangement and bonding together of proteins and centromeric DNA molecules to form a centromeric protein-DNA complex. Includes the formation of the chromatin structures which form a platform for the kinetochore, and assembly of the kinetochore onto this specialized chromatin. In fission yeast and higher eukaryotes this process also includes the formation of heterochromatin at the outer repeat (pericentric) regions of the centromere." [GOC:mah, GOC:vw] synonym: "centromere assembly" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb] synonym: "centromere organization" EXACT [GOC:dph, PMID:18923422]

I took the definition from the above. My take is that 'centromere complex' differs from 'kinetochore' in that the former is, as in the def. above, a chromatin structure which forms a platform for the kinetochore. The centromere complex is a protein-DNA complex, while the kinetochore is a protein complex. I hope this makes sense, but let me know if not - or if you'd have suggestions on how to add to the definition.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hmm I think this new term is equivalent to

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000775 chromosome, centromeric region

I still don't really understand why we can't just call both of these terms what biologists call them

"centromere" and "centromere assembly" and make the other terms synonyms

Note that GO:0000775 has related synonym "centromere" but couldn't this be exact? centromere complex assembly has exact synonym "centromere assembly" (these could be switched?)

Part of the problem is the historical confusion between "centromere sequence" in SO and "centromere" as used to describe the protein DNA complex as in CC.....but maybe we can figure this out?

Original comment by: ValWood

[gocentral]

Hi Val,

I agree that 'centromere complex' and 'chromosome, centromeric region' look quite similar. I could merge the former into the latter (and make 'chromosome, centromeric region' is_a protein-DNA complex, and - note for self - edit the xp file so that 'centromere complex assembly' points to 'chromosome, centromeric region'. I'd also give it an exact synonym 'chromosome, centromeric region assembly'.)

The obsoletion comment for 'centromere' says "This term was made obsolete because it is a genetically defined region and not a specific subcellular localization." based on the obsoleted term def. "OBSOLETE. The region of a eukaryotic chromosome that is attached to the spindle during nuclear division. It is defined genetically as the region of the chromosome that always segregates at the first division of meiosis; the region of the chromosome in which no crossing over occurs. At the start of M phase, each chromosome consists of two sister chromatids with a constriction at a point which forms the centromere. During late prophase two kinetochores assemble on each centromere, one kinetochore on each sister chromatid."

I guess that's where the synonym scope comes from.

If we merge as suggested above, I think we should be fine...

Paola

Original comment by: paolaroncaglia

[gocentral]

I will check with Midori if I misremembered anything.

Val

Original comment by: ValWood

[gocentral]

This comment isn't clear either "Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex."

Can you replace "this term" with GO:0005698 to make it clear that this refers to the obsolete term?

tks

Val

Original comment by: ValWood

[gocentral]

I've changed that comment as you suggested. Paola

Original comment by: paolaroncaglia

[gocentral]

Summary of email correspondence: Midori didn't actually work on those terms, and David and Tanya agree with my proposal, so I've gone ahead and implemented it.

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-fixed

Original comment by: paolaroncaglia