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NTR: centromere assembly related #5065

Closed gocentral closed 9 years ago

gocentral commented 16 years ago

suggested we need a term 'centromere assembly" as a broader parent of both kinetochore assembly and chromatin remodeling at centromere

Other points:

we refer to

kinetochore as "located at the pericentric region of DNA"

and

have a term

GO:0000775 : chromosome, pericentric region
The central region of a chromosome that includes the centromere and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.

For pombe and higher eukaryotes (with modular centromeres), the pericentric region of the chromsosome referes to the outer repeats of the centromere (as opposed to the central core, so this terminalogy is confusing for us...)


Well, both possibily, we don't know which one yet. You don't have a "centromere assembly" category, eh?

> so would > > kinetochore assembly > The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules. > http://www.ebi.ac.uk/ego/GTerm?id=GO:0051382 > > or > http://www.ebi.ac.uk/ego/GTerm?id=GO:0031055 > chromatin remodeling at centromere > Dynamic structural changes in centromeric DNA

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/5082":https://sourceforge.net/p/geneontology/ontology-requests/5082

gocentral commented 16 years ago

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Note to self, update Mst1 check other associations maybe should move up....

Original comment by: ValWood

gocentral commented 16 years ago

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Hi Val,

The centromere, at least in cerevisiae, is a discreet region of DNA and there isn't really any "assembly" involved. So I'm not sure what process the term "centromere assembly" is covering. What would be the definition of the term?

Jodi

Original comment by: jodih

gocentral commented 16 years ago

Logged In: YES user_id=516865 Originator: YES

Hi,

I didn't really provide enough information here. The term I need is 'centromere complex assembly' There are 2 terms which I usually use for 'centromere complex assembly'

i)kinetochore assembly The aggregation, arrangement and bonding together of a set of components to form the kinetochore, a multisubunit complex that is located at the pericentric region of DNA and provides an attachment point for the spindle microtubules.

or ii) centric heterochromatin formation The assembly of chromatin into heterochromatin near the centromere. (or its parent chromatin remodelling at the centromere)

The problem (confirmed by Susan Forsburg who suggested the new term) that we do not always know which of these sub processes of centromere complex formation are affected and we need a common parent term (and an additional process).

Also, these terms are currently unconnected in the graph, except by chromosome organization and biogenesis)

the new term centromere complex assembly would be a parent of the above terms, and a new 3rd term (also suggested by Susan) iii) NTR centric core chromatin formation, defined by the presence of the variant histone CENP-A (this would include processes like CenpA-loading)

A proposed definition for the new 'chromosome complex assembly' term The formation of the chromatin structures which form a platform for the kinetochore, and assembly of the kinetochore onmto this specialsed chromatin. In fission yeast and higher eukaryotes this process also includes the formation of heterochromatin at the pericentric regions of the centromere (outer repeats).

so i) kinetochore assembly (kinetochore referring only to the proteinaceous part of the centromere) ii) centric heterochromatin formation (present in organisms with modular centromeres, anmd includes all of the RNAi pathway stuff) iii) NTR centric core chromatin formation (present in pombe, cerevisia and metazoa)

Note cerevisiae does not have ii) which refers to the heterochormatic outer repeats of the centromere more commonly referred to as the 'pericentric region'

The knock on effects of this.

i) Possibly new term names for those which use 'pericentric' which means something different for organisms with modular centromeres than its current meaning in GO, and is known to be confusing to the pombe centromere community.

ii) reassignment of synonyms will be required. For instance kinetochore assembly currently has synonyms: narrow centromere and kinetochore complex maturation narrow centromere/kinetochore complex maturation (which don't seem to be narrow....)

Hoepfully I have meade this sclearer (I didn't even understand yeasterdays psoting myself!)

Also this was published this week. Should be V. useful for this item....

Partridge JF. Centromeric chromatin in fission yeast. Front Biosci. 2008 May 1;13:3896-905. PMID: 18508483 Outlines the main processes, which are mostly conserved.

Val

Original comment by: ValWood

gocentral commented 16 years ago

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also see SF 1219716, on the different meanings of 'pericentric' ... would be good to sort all out together if possible

Original comment by: mah11

gocentral commented 16 years ago

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I think this scheme looks good. Ultimately, it will look like this, right?:

centromere complex assembly

I took a look at the paper you referenced and at a CSE4 paper for cerevisiae, and these terms seem to cover what's going on.

I think your proposed definition for 'centromere complex assembly' also works.

Jodi

Original comment by: jodih

gocentral commented 16 years ago

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added centromere complex assembly GO:0034508 centromeric core chromatin formation GO:0034509

added relationships centromeric heterochromatin formation GO:0031508 part_of GO:0034508 kinetochore assembly GO:0051382 part_of GO:0034508

Original comment by: mah11

gocentral commented 16 years ago

Original comment by: mah11

gocentral commented 13 years ago

Original comment by: mah11