gocentral
commented
15 years ago Re Sin3 complex(es): at the moment GO:0016580 is defined as a single complex. If you want to move other terms to be its children, we should rejig the def to make it more consistent with being a grouping term. Do you have any recommendations or preferences for how we word the new def? (If not, I can wing it based on the review.)
Regarding term names for GO:0032221 and GO:0033698, I really have no preference, but Val and Rama hashed out the current names in SFs 2435061 and 2435063 (links below). We ought to check with them before making any further changes; I'll email.
https://sourceforge.net/tracker/index.php?func=detail&aid=2435061&group\_id=36855&atid=440764 https://sourceforge.net/tracker/index.php?func=detail&aid=2435063&group\_id=36855&atid=440764
For everything else, I'm happy to trust your more recent attention to the relevant literature. I'll make the changes when we really have CVS access back (getting time-outs today).
cheers, m
Original comment by: mah11
I’d like to suggest some changes (and one new term) to clean up the relationships between different types of histone deacetylase complexes. With these changes (detailed below), the complexes found in S. cerevisiae will be accurately represented.
However, while researching this topic, I realized that more extensive changes would probably be necessary to accurately represent the much wider array of HDACs found in mammals and other “larger” organisms. I’m not suggesting these further changes at this time, because I don’t actually need them for my organism, and I don’t necessarily understand the biology involved…if someone else is interested, I found the following review helpful! Yang XJ, Seto E (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9(3):206-18 PubMed ID: 18292778
GO:0000118 : histone deacetylase complex
Change parentage: Make histone deacetylase a child of “GO:0016585 : chromatin remodeling complex”, rather than a sibling of this term
GO:0016580 : Sin3 complex
Change parentage: Make Sin3 complex a child of “GO:0000790 : nuclear chromatin” in addition to current parentage. From the reading of the current definition, it may have been intentional to not include chromatin as a parent; however, whenever components of the Sin3-like complexes are listed in the literature, they always seem to include the histone-binding proteins (e.g. pho23 in yeast or ING1/2 in mammals), so it seems appropriate to have this as a child of nuclear chromatin.
GO:0033698 : Rpd3/Clr6 histone deacetylase complex I/I' (aka Rpd3L complex)
Change parentage: Make Rpd3L complex a child of “GO:0016580 : Sin3 complex” rather than a direct child of “GO:0000118 : histone deacetylase complex”
Also, would it be possible that the name of this term be changed back to the original (Rpd3L complex) with “Rpd3/Clr6 histone deacetylase complex I/I'” as a synonym? Rpd3L complex is the much, much more common term in the literature.
GO:0032221 : Rpd3/Clr6 histone deacetylase complex II' (aka Rpd3S complex)
Change parentage: Make Rpd3S complex a child of “GO:0016580 : Sin3 complex” rather than a direct child of “GO:0000118 : histone deacetylase complex”
As above, would it be possible that the name of this term be changed back to the original (Rpd3S complex) with “Rpd3/Clr6 histone deacetylase complex II'” as a synonym? Rpd3S complex is the much, much more common term in the literature.
GO:0070210 : Rpd3L-Expanded complex
Change parentage: Make Rpd3L-Expanded complex a child of “GO:0000118 : histone deacetylase complex” rather than a direct child of “GO:0016585 : chromatin remodeling complex”.
There is also a typo in the definition of this complex. “…histone deacetyltransferase” should be changed to “histone deacetylase”.
GO:0070211 : Snt2C complex
Change parentage: Make Snt2C complex a child of “GO:0000118 : histone deacetylase complex” rather than a direct child of “GO:0016585 : chromatin remodeling complex”.
New Term Request: HDA1 complex
A tetrameric Class II histone deacetylase complex. In S. cerevisiae it is composed of two Hda1p subunits along with Hda2p and Hda3p.
Child of “GO:0000118 : histone deacetylase complex” and “GO:0016585 : chromatin remodeling complex”.
References: PMID: 8663039, PMID: 11287668
GO:0016581 : NuRD complex
I don’t think that this complex is actually the same as the “SHREC” complex that is found in pombe. I’ve read several papers that say the NuRD complex isn’t found in fungi (e.g. PMID: 10589671, PMID: 18292778). The “SHREC” reference listed as a reference for the definition actually only mentioned NuRD in the discussion section and seemed to me to be comparing the two complexes rather than saying they were equivalent. Their exact wording is that the SHREC complex is “reminiscent” of the NuRD complex. So, I think that it would be better to make SHREC it’s own complex (sibling of NuRD) and remove references to fungi from the definition.
When it’s all done, it should look something like this (including only mentioned terms and parents):
GO:0016585 : chromatin remodeling complex GO:0000118 : histone deacetylase complex GO:0016580 : Sin3 complex GO:0033698 : Rpd3L complex GO:0032221 : Rpd3S complex GO:0070210 : Rpd3L-Expanded complex GO:0070211 : Snt2C complex New: HDA1 complex
GO:0000790 : nuclear chromatin
GO:0016580 : Sin3 complex GO:0070210 : Rpd3L-Expanded complex GO:0070211 : Snt2C complex New: HDA1 complex
Reported by: diannafisk
Original Ticket: geneontology/ontology-requests/6310