[Go] MT attachment to chromosome
Jodi Hirschman
jodi at genome.stanford.edu
Wed Nov 26 15:05:43 PST 2008
Hi all,
SGD curators discussed this issue today. We've been following the
thread, but none of us is particularly knowledgeable in this area and
we support your plan to ask an expert in the field. We'll stay
tuned...
Jodi
On Nov 24, 2008, at 8:17 AM, Lisa Matthews wrote:
> 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
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
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>>
>>
>
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