histone ubiquitination

[gocentral]

we have

GO:0016574 : histone ubiquitination --GO:0010390 : histone monoubiquitination

I want to capture that the experiments I'm annotating refer to

histone H2B K120 ubiquitination (I used K120, the human residue but this is K123 in bidding yeast/K119 in fission yeast)

should we have anew term?

The only troube is that as far as I know histone H2B K120 is the only known histone target of ubiquitin, does this matter?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4293":https://sourceforge.net/p/geneontology/ontology-requests/4293

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Actually the poster on my wall informs me that human H2A is also ubiqutinated at 118K

Original comment by: ValWood

[gocentral]

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Hmmm, doesn't really seem worth adding one specific child term if that's the only specific type known. Might be more worth expanding the explanatory definition of the "histone monoubiquitination (GO:0010390)" term to include the info you give about what is currently known.

-Karen

Original comment by: krchristie

[gocentral]

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I just found this so I think we should add them.

Val

Although histone ubiquitylation has been known for more than three decades (Goldknopf et al., 1975), its functional significance remained elusive until very recently (Osley, 2004). Yeast histone H2B is ubiquitylated at lysine 123 (equivalent to lysine 120 in mammals), and uH2B accounts for about 10% of total cellular H2B (Robzyk et al., 2000). Rad6 and Bre1 have been identified as the ubiquitin conjugating and ligation enzymes responsible for this modification (Hwang et al., 2003, Robzyk et al., 2000 and Wood et al., 2003). Subsequent studies have demonstrated a role for H2B ubiquitylation in transcriptional activation (Henry et al., 2003 and Kao et al., 2004). Furthermore, deletion of H2B deubiquitinase Ubp10 impairs silencing at telomere and rDNA regions (Emre et al., 2005 and Gardner et al., 2005). Interestingly, H2B ubiquitylation was found to be required for subsequent methylation of H3K4 and H3K79 (Briggs et al., 2002, Dover et al., 2002, Ng et al., 2002 and Sun and Allis, 2002), suggesting a role for H2B ubiquitylation in the regulation of other histone modifications and chromatin function. Recently, it has been shown that RNF20/40, the mammalian counterpart of Bre1, possesses ubiquitin ligase activity for histone H2B and that H2B ubiquitylation could regulate H3K4 and H3K79 methylation (Kim et al., 2005 and Zhu et al., 2005), indicating that the role of H2B ubiquitylation in transcription is evolutionally conserved. In addition to transcription, H2B ubiquitylation has recently been implicated in meiotic recombination and DNA damage checkpoint control (Giannattasio et al., 2005 and Yamashita et al., 2004).

Original comment by: ValWood

[gocentral]

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All very interesting and important, but it's still just more details about H2B K120 (or equivalent) ubiquitination. To add child terms, we would really prefer to have more than one, because otherwise what's the difference between the parent and the child?

If you can track down anything about that H2A ubiquitination, and especially if it's carried out by different gene products from the H2B ubiquitination, then we'd have a good case for adding child terms.

m

Original comment by: mah11

[gocentral]

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oops sorry, I misread that. I thougth it was talking about an additioanl H3 ubiquitination but this is the methylation.

One source of the info for H2A ubiqutination was

http://www.sciencedirect.com/science?\_ob=MImg&\_imagekey=B6WSN-4N3XF1K-N- 1&_cdi=7051&_user=776054&_coverDate=02%2F23%2F2007&_sk=%23TOC%237051%232 007%23998719995%23644913%23FLA%23display%23Volume_128,_Issue_4,_Pages62 7-802(23_February_2007)%23tagged%23Volume%23first%3D128%23Issue%23first %3D4%23date%23(23_February_2007)%23&view=c&_gw=y&wchp=dGLbVzb-zSkzk&md5= 2fa74795c1df7eddb4cc1ae9a379afe0&ie=/sdarticle.pdf

Original comment by: ValWood

[gocentral]

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I found a paper which describes a H2A modification. its a fly gene and appears to be called Ring1b but I can't find this in Flybase, so I don't know if its a different gene or not. I can't find any other fly identifier for this protein. I think it is different gene products because its described as polycomb family and I don't think this family is in yeasts.

I'm going to finish these papers today, shall I just go with histone ubiquitination?

http://www.jbc.org/cgi/content/full/279/51/52812

Original comment by: ValWood

[gocentral]

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added histone H2A ubiquitination GO:0033522 histone H2B ubiquitination GO:0033523

Original comment by: mah11

[gocentral]

• labels: --> New term request
• milestone: --> 224410
• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11