ntr: histone exchange

[gocentral]

the replacement of resident histones which results in altered chromatin states as a result of the removal of histone modifications

(I cobbled this def from a EMBO report PMID: 15809658 i'm sure it can be improved...nmo hurry for this but I know I have a note that I need this term for something)

synonym histone replacement

the existing terms

fertilization, exchange of chromosomal proteins and spermatogenesis, exchange of chromosomal proteins

should be children of this general term

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/2772":https://sourceforge.net/p/geneontology/ontology-requests/2772

[gocentral]

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Hi Val - presumably this new term would be a child of 'chromatin remodeling ; GO:0006338'?

Original comment by: jl242

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> jl242

Original comment by: jl242

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I think so

val

Original comment by: ValWood

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Modified the def (from PMID:15066277 and PMID: 11735001):

The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits.

Comment: Note that this term also includes the exchange of sperm-specific histones or protamines with histones, occurring during spermatogenesis and fertilization.

That sound okay?

Original comment by: jl242

[gocentral]

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Actually, I think the new term can go under 'ATP-dependent chromatin remodeling' because they all seem to require ATP...

Original comment by: jl242

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yep

Original comment by: ValWood

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Added 'histone exchange ; GO:0043486' as child of 'ATP-dependent chromatin remodeling ; GO:0043044' and with children 'fertilization, exchange of chromosomal proteins ; GO:0035042' 'spermatogenesis, exchange of chromosomal proteins ; GO:0035093'.

Original comment by: jl242

[gocentral]

• labels: --> New term request
• status: open --> closed-accepted

Original comment by: jl242

[gocentral]

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Added 'histone exchange ; GO:0043486' as child of 'ATP-dependent chromatin remodeling ; GO:0043044' and with children 'fertilization, exchange of chromosomal proteins ; GO:0035042' 'spermatogenesis, exchange of chromosomal proteins ; GO:0035093'.

Original comment by: jl242

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Hi jane,

I wonder if it is confusing to heave the child term refer to exchange of chromosomal proteins and the parent term to exchange of histone proteins

(although the defs for the 'chromosomal protein exchange' do appear to refer to histones or histone varients.

I wonder if the term names should be standardized?

val

Original comment by: ValWood

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Hi Val - the child terms have exact synonyms with 'histone' instead of 'chromosomal protein', but yes, might make sense to make the the same. I think the reason the child terms are chromosomal protein is that sperm chromatin uses special non-histone proteins in its chromatin...but I think using histone is more intuitive...what do you think?

Original comment by: jl242

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hmm, sounds as though 'histones' are still exchanged, but it might be worth asking somebody who has used/created these terms....

I just did a Google search and with "exchange of chromosomal proteins" I only retreive the GO terms, but if i search on "histone exchange" and "sperm" I get lots of hits to

histone exchange and specifically "protamine-histone exchange" which seem to be referring to this process. So it seems to make sense?

Original comment by: ValWood