ntrs: kinetochore localization

[gocentral]

id: GO:new1 name: kinetochore localization def: "A cellular localization process in which a kinetochore is transported to, and/or maintained in, a specific location." [GOC:mah] is_a: GO:0034629 ! cellular protein complex localization is_a: GO0051640 ! organelle localization (based on parentage of kinetochore GO:0000776)

id: GO:new2 name: kinetochore clustering at spindle pole body def: "A cellular localization process in which kinetochores are transported to, and/or maintained in, a location near the spindle pole body." [GOC:mah, PMID:21965289] synonym: "kinetochore clustering at SPB" EXACT [GOC:mah] synonym: "centromere-SPB clustering" RELATED [GOC:vw, PMID:18158900] is_a: GO:new1

GO:new2 has been observed in fission yeast; I have no idea whether it's applicable to other taxa, or if it should have a restriction.

Inspired by some mutant phenotypes for which a FYPO term request is pending -- see https://sourceforge.net/tracker/?func=detail&aid=3586738&group\_id=65526&atid=2096431 and https://sourceforge.net/tracker/?func=detail&aid=3587563&group\_id=65526&atid=2096431

I can add these if you're happy to have them go in without changes or other complications.

Thanks, m

Reported by: mah11

Original Ticket: geneontology/ontology-requests/9866

[gocentral]

I wonder how this should relate to GO:0008608 attachment of spindle microtubules to kinetochore

it can't be name: kinetochore clustering at spindle pole body part of GO:0008608 attachment of spindle microtubules to kinetochore

maybe its name: kinetochore clustering at spindle pole body has_part GO:0008608 attachment of spindle microtubules to kinetochore

but it doesn't seem quite right either. I haven't got the events quite straight in my head.....

Original comment by: ValWood

[gocentral]

Hi,

Midori, I'm happy with your suggested stanzas if you want to add them in, thank you. The only thing I'd add is a synonym for GO:new2:

synonym: "kinetochore localization at spindle pole body" EXACT

I wouldn't know about a taxon rule for GO:new2 either, so I'd leave it unless someone asks for it and/or can provide a reference.

Val, I don't think we can add a link between those two terms as they are, because I think they are separated in time. Maybe GO:NEW [one term] involved_in [the other term] but would that be really needed? Anything you might annotate to it?

I'm assigning this item to Midori so she can add her terms in. Should you opt to create a new term as above, you might use TermGenie I think. Any comments let me know.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: paolaroncaglia

[gocentral]

added kinetochore localization GO:0072765 kinetochore clustering at spindle pole body GO:0072766

as in original, plus Paola's suggested synonym for GO:0072766

I'll leave it without a taxon constraint until we know more.

thanks! m

Original comment by: mah11

[gocentral]

• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

Yes sorry ignore my comment this is unrelated.

Original comment by: ValWood

[gocentral]

Based on this feedback from Jonathan Miller:

> 1. Nsk1 is required for stable association of kinetochores with the spindle pole during anaphase B. After this time Nsk1 disappears so the continued clustering of kinetochores with the spindle pole during the following interphase is independent of Nsk1. In this weeks Journal Cell Biology Songtao Jia and Fred Chang show that this is due to another protein, Csi1 (SPBC2G2.14). > If cells enter mitosis with unclustered kinetochores then the kinetochores need to be retrieved by a process involving the DASh complex. So is Nsk1 involved in attachment of kinetochores to spindle microtubule? Yes - but possibly indirectly. I personally would merge these two terms and add 2. below as the other term. > 2. There are four proteins in which "abnormal clustering of kinetochores to spindle pole bodies" has been demonstrated. These are crm1, mto1, nsk1, and now csi1 (Funabiki et al., 1993; Franco et al., 2007; Buttrick et al., 2011; Huo et al., 2012). The original paper on ima1 by the Globel lab. in Cell in 2008 has been shown to be incorrect by Hiraoka and colleagues (King et al., 2008; Hiraoka et al., 2011) so Ima1 should not be put in this class. Note also that this must be distinct from the natural unclustering of kinetochores from spindle poles that is observed during telomere bouquet formation in meiosis.

re the taxon contraint: "Budding yeast kinetochores remain attached to the old SPB throughout the cell cycle via short micro- tubules. After S phase, both sister kinetochores initially bind to microtubules from the same (old) SPB and therefore need to be reoriented during mitosis to establish biorientation (Biggins et al., 1999; Kitamura et al., 2007). By contrast, in fission yeast, the SPB defenestrates from the nuclear envelope at the end of anaphase B, yet kinetochores remain clustered near the SPB via a nonmicrotu- bule-based linkage (Ding et al., 1997). The molecular nature of this linkage is unclear but is thought to involve the transmembrane protein Ima1, which binds indirectly to the heterochromatic region of centromeres, and other, as-yet-unknown proteins that link the outer kinetochore to the inner face of the SPB (King et al., 2008). In this paper, we reveal that association of kinetochores to SPBs during anaphase B is necessary to maintain accurate chromosome segregation, and we identify a novel substrate of the Clp1 phos- phatase, Nsk1, that binds to the kinetochore–SPB junction during anaphase B to facilitate this process."

So the process of clustering occurs in both yeast, but the mechanism is different....

A couple of refinements to the term

Because a different clustering process occurs during telomere boquet formation, and because it is old spindle pole body specific could we change to "kinetochore clustering at the old mitotic spindle pole body" so we don't need to disambiguate later.

Val

Original comment by: ValWood

[gocentral]

opening for small term name tweaks

Original comment by: ValWood

[gocentral]

• status: closed-accepted --> open-accepted

Original comment by: ValWood

[gocentral]

• assigned_to: gomidori --> nobody

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> paolaroncaglia
• status: open-accepted --> open

Original comment by: paolaroncaglia

[gocentral]

Hi Val,

So if I understand correctly, you'd want the name of kinetochore clustering at spindle pole body GO:0072766 changed to kinetochore clustering at the old mitotic spindle pole body and the def. adjusted accordingly.

Before I proceed, could you please confirm that nothing else needs to be done? (My doubt stems from your latest comment 'opening for small term name tweaks'). Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Yes sorry the def does need adjusting too. val

Original comment by: ValWood

[gocentral]

Edited term name, definition and synonyms' scope accordingly. The stanza now reads.

[Term] id: GO:0072766 name: kinetochore clustering at the old mitotic spindle pole body namespace: biological_process def: "A cellular localization process in which kinetochores are transported to, and/or maintained in, a location near the old mitotic spindle pole body." [GOC:mah, GOC:vw, PMID:21965289] synonym: "centromere-SPB clustering" RELATED [GOC:vw, PMID:18158900] synonym: "kinetochore clustering at SPB" RELATED [GOC:mah] synonym: "kinetochore clustering at spindle pole body" RELATED [] synonym: "kinetochore localization at spindle pole body" RELATED [GOC:pr] is_a: GO:0072765 ! kinetochore localization

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia

[gocentral]

Sorry Paola I had a couple of more thought about the "name: kinetochore clustering at old mitotic spindle pole body" term based on a new paper I'm reading: PMID:23166349

"One of the most striking examples of genome organization is the Rabl-like configuration of chromosomes in the interphase nuclei, in which centromeres are clustered at the nuclear periphery. This clustering has been seen in diverse cell types ranging from yeast, to plants, to flies (Funabiki et al., 1993; Jin et al., 1998; Fang and Spector, 2005)." In interphase fission yeast cells, chromosomes are attached by their centromeres to the inner nuclear envelope near the region of the spindle pole body

First I see the parent of "kinetochore clustering" is kinetochore localization which seemed right, but really the entire chromosome is localized (process is also called centromere clustering), so maybe instead

rename as "centromere clustering at the nuclear periphery" and should be a child of chromosome localization instead ?

Suggested def: A cellular localization process in which kinetochores/centromeres are transported to or maintained in the nuclear periphery. This process is responsible for the Rabl-like configuration of chromosomes in the interphase nuclei. In fission yeast this occurs at a location near the old mitotic spindle pole body (but we don't need to mention the SPB in the term name to make it more generic)

val

Original comment by: ValWood

[gocentral]

• status: closed-accepted --> open-accepted

Original comment by: ValWood

[gocentral]

Hi Val,

This is done. The stanza now reads:

[Term] id: GO:0072766 name: centromere clustering at the nuclear periphery namespace: biological_process def: "A cellular localization process in which kinetochores/centromeres are transported to or maintained in the nuclear periphery. This process is responsible for the Rabl-like configuration of chromosomes in the interphase nuclei. In fission yeast this occurs at a location near the old mitotic spindle pole body." [GOC:mah, GOC:vw, PMID:21965289, PMID:23166349] synonym: "centromere-SPB clustering" RELATED [GOC:vw, PMID:18158900] synonym: "kinetochore clustering at SPB" RELATED [GOC:mah] synonym: "kinetochore clustering at spindle pole body" RELATED [] synonym: "kinetochore clustering at the old mitotic spindle pole body" RELATED [] synonym: "kinetochore localization at spindle pole body" RELATED [GOC:pr] is_a: GO:0050000 ! chromosome localization created_by: midori creation_date: 2012-11-21T13:32:22Z

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open-accepted --> closed-accepted

Original comment by: paolaroncaglia