[Go] MT attachment to chromosome
Lisa Matthews
lmatthew at cshl.edu
Mon Nov 24 05:17:45 PST 2008
Sure, I'll ask Iain about the timing. His other Nature MCB review
from this year (PMID: 18097444) has a nice table of orthologs/predicted
orthologs to the human kinetochore proteins/complexes in the
supplementary materials in case it could be helpful for the reference
genome annotations.
Best,
Lisa
Valerie Wood wrote:
> Hmm, I don't know. Kinetochore assembly occurs from S-phase to early mitosis. I don't know when these complexes are assembled into the kinetochore temporally ....However as they form a bridge between kinetochore and microtubules they probably assemble late.
>
> It might also be worth checking the positioning and parentage of
> DASH
> COMA
> MIs12/MIND
>
> Kinetochore proteins might be a good set to tackle together for reference geneome annotation. Particularly as a large number have been partially characterised over the past few years, and they are generally conserved (although the levels of conservation are low and difficult or impossible to detect with reciprocal best hits).
>
> VAl
>
>
>
> Midori Harris <midori at ebi.ac.uk> wrote:
>
>> Hi Lisa,
>>
>> Although I added the terms, I don't have any specialist knowledge about
>> these complexes, so most likely I put them under the more generic parent
>> because I wasn't completely confident that the more specific parent would
>> always be correct.
>>
>> Maybe it would be good to put the question to Iain along with the rest --
>> unless the SGD curators or Val know of anything more specific. In any
>> case, if the verdict is that the terms should be moved down to part_of
>> condensed chromosome kinetochore, that'll be easy to do.
>>
>> Midori
>>
>> On Fri, 21 Nov 2008, Lisa Matthews wrote:
>>
>>
>>> Hi Midori,
>>> I know, it's good to be back in touch! I'm back in the USA now.
>>> , I just had one question before popping the question over to Iain. Based on
>>> the definition of Ndc80 complex and NMS Complex (and the fact that Ndc80
>>> associates with the kinetochore only during mitosis), I would have thought
>>> that these terms would be "part of" condensed chromosome kinetochore rather
>>> that the more generic kinetochore or am I missing something(?)
>>>
>>> * part_of relationship GO:0000776 : kinetochore [234 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000776&session_id=7795amigo1227278122>
>>>
>>> *
>>> o close
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=minus_node&target=GO:0000777&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
>>> is_a relationship GO:0000777 : condensed chromosome
>>> kinetochore
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000777&session_id=7795amigo1227278122>
>>> [134 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000777&session_id=7795amigo1227278122>
>>>
>>> o
>>> + open
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000778&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
>>> is_a relationship GO:0000778 : condensed nuclear
>>> chromosome kinetochore
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000778&session_id=7795amigo1227278122>
>>> [69 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000778&session_id=7795amigo1227278122>
>>>
>>> + open
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000939&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
>>> part_of relationship GO:0000939 : inner kinetochore of
>>> condensed chromosome
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000939&session_id=7795amigo1227278122>
>>> [34 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000939&session_id=7795amigo1227278122>
>>>
>>> + open
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000444&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
>>> part_of relationship GO:0000444 : MIS12/MIND type
>>> complex
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000444&session_id=7795amigo1227278122>
>>> [18 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000444&session_id=7795amigo1227278122>
>>>
>>> + leaf node part_of relationship GO:0033551 : monopolin
>>> complex
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0033551&session_id=7795amigo1227278122>
>>> [8 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0033551&session_id=7795amigo1227278122>
>>>
>>> + open
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?action=plus_node&target=GO:0000940&term=GO:0000776&open_1=GO:0000777,GO:0000776&session_id=7795amigo1227278122#lineage>
>>> part_of relationship GO:0000940 : outer kinetochore of
>>> condensed chromosome
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0000940&session_id=7795amigo1227278122>
>>> [17 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0000940&session_id=7795amigo1227278122>
>>>
>>> o leaf node part_of relationship GO:0031262 : Ndc80 complex
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0031262&session_id=7795amigo1227278122>
>>> [16 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0031262&session_id=7795amigo1227278122>
>>>
>>> o leaf node part_of relationship GO:0031617 : NMS complex
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0031617&session_id=7795amigo1227278122>
>>> [13 gene products]
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0031617&session_id=7795amigo1227278122>
>>>
>>> :
>>> Ndc80 Complex
>>> A supercomplex formed by the association of two subcomplexes (known as MIND
>>> and Ndc80 in Schizosaccharomyces) with additional proteins at the
>>> kinetochores of condensed nuclear chromosomes. [source: PMID:16079914
>>> <http://www.ncbi.nlm.nih.gov/pubmed/16079914>]
>>>
>>> NMS Complex:
>>> A supercomplex formed by the association of two subcomplexes (known
>>> as MIND and Ndc80 in Schizosaccharomyces) with additional proteins
>>> at the kinetochores of condensed nuclear chromosomes. [source:
>>> PMID:16079914 <http://www.ncbi.nlm.nih.gov/pubmed/16079914>]
>>>
>>> Thanks,
>>> Lisa
>>>
>>>
>>> Midori Harris wrote:
>>>
>>>> Hi Lisa,
>>>>
>>>> It would be great if you could ask Iain Cheeseman what he thinks. We seem
>>>> to be converging on agreeing that kinetochore-port_of-chromosome is the
>>>> best we can do for now, until we implement more relationship types, but it
>>>> can't hurt to get an expert's view.
>>>>
>>>> (Great to hear fraom you again, too -- it's been a while!)
>>>>
>>>> Midori
>>>>
>>>> On Fri, 21 Nov 2008, Lisa Matthews wrote:
>>>>
>>>>
>>>>> Hi all,
>>>>> There is a really good review that just came out on this written by the
>>>>> Cheeseman group (they've done a lot on defining the highly conserved
>>>>> kinetochore DNA to microtubule molecular connectivity PMID: 19000831. I
>>>>> can run this question by Iain Cheeseman who has recently helped Reactome
>>>>> out with some annotations on centrosome function.
>>>>> Lisa
>>>>>
>>>>> Valerie Wood wrote:
>>>>>
>>>>>> Currently a placement of kinetochore under chromosome would be correct
>>>>>> based on how condensed nuclear centromeric region is defined
>>>>>>
>>>>>> def
>>>>>> condensed nuclear chromosome, centromeric region
>>>>>> The region of a condensed chromosome in the nucleus that includes the
>>>>>> centromere and associated proteins, including the kinetochore. In
>>>>>> monocentric chromosomes, this region corresponds to a single area of the
>>>>>> chromosome, whereas in holocentric chromosomes, it is evenly distributed
>>>>>> along the chromosome.
>>>>>>
>>>>>> which is a child of chromosome
>>>>>> although at present kinetochore is not a child of this term
>>>>>>
>>>>>> I don't know what is right though.
>>>>>>
>>>>>> VAl
>>>>>>
>>>>>> Midori Harris <midori at ebi.ac.uk> wrote:
>>>>>>
>>>>>>> I think what would really help are those spatial relationship types that
>>>>>>> we've talked about with Chris. Kinetochore-chromosome is one of many
>>>>>>> cases where I suspect that biologists would expect to see some
>>>>>>> connection (tho I'm sure Rex or Val can correct me if I'm wrong), so
>>>>>>> we've used part_of even though it's far from ideal.
>>>>>>>
>>>>>>> m
>>>>>>>
>>>>>>> On Fri, 21 Nov 2008, David Hill wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> I'm not sure the kinetochore should be a part_of the chromosome. It
>>>>>>>> attaches to the centromere, which is part of the chromosome. I think
>>>>>>>> we might want to have Rex weigh in on this too. He's a cell biologist.
>>>>>>>>
>>>>>>>> David
>>>>>>>>
>>>>>>>> Midori Harris wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> Working on some cross-product definitions, I came up with a question
>>>>>>>>> about whether two terms that are currently siblings should have an
>>>>>>>>> is_a link. The terms are:
>>>>>>>>>
>>>>>>>>> attachment of spindle microtubules to chromosome GO:0051313
>>>>>>>>> attachment of spindle microtubules to kinetochore GO:0008608
>>>>>>>>>
>>>>>>>>> and I think we shoud have GO:0008608 is_a GO:0051313 because
>>>>>>>>> kinetochore is part_of chromosome in the component ontology.
>>>>>>>>>
>>>>>>>>> I've opened a SourceForge item, and I'd appreciate any comments.
>>>>>>>>>
>>>>>>>>> https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2320413&group_id=36855
>>>>>>>>> thanks,
>>>>>>>>> midori
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Go mailing list
>>>>>>>>> Go at geneontology.org
>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>>>>
>>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Go mailing list
>>>>>>> Go at geneontology.org
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>
>
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