FACT complex - definition refinement

[gocentral]

Hi,

I think we meed to modify the definition of the "FACT complex ; GO: 0035101"

Currently, it is this:

Definition: An abundant nuclear complex, which was identified as a chromatin-specific factor required for transcription elongation on chromatin templates. FACT is composed of two proteins that are evolutionarily conserved in all eukaryotes and homologous to yeast Spt16p and Pob3p.

But the intro to this paper, PubMed ID: 16678108, says this:

FACT (facilitates chromatin transcription) is an essential chromatin reorganizing factor (Belotserkovskaya and Reinberg, 2004, Formosa, 2002 and O'Donnell et al., 2004). The complex from the yeast S. cerevisiae, yFACT, is composed of three proteins: Spt16/Cdc68 (120 kDa), Pob3 (63 kDa), and Nhp6 (11 kDa). FACT subunits are highly conserved among eukaryotes, although in metazoans the Pob3 and Nhp6 orthologs are fused to form SSRP1. Of these components, only the structure of the nonspecific DNA binding protein Nhp6 has been reported (Allain et al., 1999 and Masse et al., 2002).

so maybe the definition could be changed like this:

Definition: An abundant nuclear complex, which was identified as a chromatin-specific factor required for transcription elongation on chromatin templates. In S. cerevisiae, the complex is composed of three proteins: Spt16 (120 kDa), Pob3 (63 kDa), and Nhp6 (11 kDa). FACT subunits are highly conserved among eukaryotes. However, in metazoans the Pob3 and Nhp6 orthologs are fused to form the SSRP1 protein.

thanks,

-Karen

Reported by: krchristie

Original Ticket: "geneontology/ontology-requests/3527":https://sourceforge.net/p/geneontology/ontology-requests/3527

[gocentral]

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sounds fine to me .. will you implement? m

Original comment by: mah11

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Yes. Implemented as suggested.

-Karen

Original comment by: krchristie

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• labels: --> Other term-related request
• assigned_to: nobody --> kchris
• status: open --> closed-accepted

Original comment by: krchristie

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Hmmm,

Having done this on Friday, today I went to tidy up some curatorial loose ends with the yeast FACT subunits and I now think that the modification I made above is not completely correct. I'm reading another paper or two:

1. PMID: 15520471 O'Donnell AF, Brewster NK, Kurniawan J, Minard LV, Johnston GC, Singer RA. Domain organization of the yeast histone chaperone FACT: the conserved N-terminal domain of FACT subunit Spt16 mediates recovery from replication stress. Nucleic Acids Res. 2004 Nov 1;32(19):5894-906. Print 2004.

2. PMID: 11432837 Formosa T, Eriksson P, Wittmeyer J, Ginn J, Yu Y, Stillman DJ. Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome- binding factor SPN. EMBO J. 2001 Jul 2;20(13):3506-17.

3. PMID: 15196460 Belotserkovskaya R, Reinberg D. Facts about FACT and transcript elongation through chromatin. Curr Opin Genet Dev. 2004 Apr;14(2):139-46. Review.

4. PMID: 15020050 Belotserkovskaya R et al. Transcription through chromatin: understanding a complex FACT. Biochim Biophys Acta. 2004 Mar 15;1677(1-3):87-99. Review.

It is true that the yeast protein Pob3, the homolog of the mammalian SSRP1 protein, lacks the HMG domain that is the domain that interacts with nuceosomes. But it's not quite a simple as the statement I quoted from the previous paper. From what I've read so far, it seems that most people talk about a 2-subunit version of the yeast FACT complex, composed of Spt16/ Cdc68 + Pob3. However, I am a little confused. For example, the Belotserkovskay et al review (#4 above; PMID: 15020050) has this statement, which basically equates BOTH the 2 subunit version of the complex (Spt16/ Cdc68 + Pob3) and the three subunit version (Spt16-Pob3-Nhp6) with the FACT complex: "Yeast FACT complex, a.k.a. CP for Cdc68–Pob3 [77] and SPN for Spt16- Pob3- Nhp6 [80], was originally purified as an entity that bound to a DNA polymerase α affinity column [72], "

However, the Formosa et al paper (#2 above) which characterizes the interaction of the 2 subunit version with the HMG domain containing protein Nhp6, indicates that Nhp6 is not "not usually in stable complexes with Spt16– Pob3", so I'm inclined to define the FACT complex as the 2 subunit complex.

On the idea that the 2-subunit complex is what should be represented, we could go with this for a definition:

Definition: An abundant nuclear complex, which was originally identified as a chromatin-specific factor required for transcription elongation on chromatin templates. The FACT complex has been shown to destablilize the interaction between the H2A/H2B dimer and the H3/H4 tetramer of the nucleosome and thus the FACT complex may play a role in DNA replication and other processes that traverse the chromatin, as well as in transcription elongation. FACT is composed of two proteins that are evolutionarily conserved in all eukaryotes and homologous to mammalian Spt16 and SSRP1. In S. cerevisiae, the Pob3 protein is homologous to SSRP1, but lacks the HMG chromatin binding domain. Instead, the yFACT complex of Spt16p and Pob3p, is recruited to nucleosomes by Nhp6p, but Nhp6p does not form a stable complex with the Spt16p/Pob3p complex.

thoughts?

-Karen

Original comment by: krchristie

[gocentral]

• status: closed-accepted --> open

Original comment by: krchristie

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In light of the additional information, I'd be happy with the latest revision.

m

Original comment by: mah11

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Hi Midori,

The more I think about this, I'm just not certain whether the yFACT complex is considered to be the 2 subunit version, the 3 subunit version, or what. Instead of making a somewhat arbitrary decision, I have written several of the corresponding authors of recent papers on yFACT to see if I can get clarification. For the moment, I'll just leave the definition of FACT as is, with the modification I just made.

thanks,

-Karen

Original comment by: krchristie

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OK :)

Original comment by: mah11

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text file transcript of email conversations with community experts

Original comment by: krchristie

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Hi,

With help from the research community, a definition has been agreed upon as the definition of the FACT complex in GO.

I sent my initial query to 4 people: David Stillman <david.stillman@path.utah.edu>, Kevin Struhl <kevin@hms.harvard.edu>, Richard Singer <Richard.Singer@Dal.ca>, Tim Formosa <Tim@biochem.utah.edu>,

Part way through the discussion, an additional person got added to the cc list. Gerald C. Johnston <G.C.Johnston@dal.ca>

Most of the responses from people were just sent to me though, not to the entire list. A full transcript of my correspondance is attached as a text file.

Here is the definition agreed upon: Definition: An abundant nuclear complex, which was originally identified in mammalian systems as a factor required for transcription elongation on chromatin templates. The FACT complex has been shown to destablilize the interaction between the H2A/H2B dimer and the H3/H4 tetramer of the nucleosome, thus reorganizing the structure of the nucleosome. In this way, the FACT complex may play a role in DNA replication and other processes that traverse the chromatin, as well as in transcription elongation. FACT is composed of two proteins that are evolutionarily conserved in all eukaryotes and homologous to mammalian Spt16 and SSRP1. In metazoans, the SSRP1 homolog contains an HMG domain; however in fungi and protists, it does not. For example, in S. cerevisiae the Pob3 protein is homologous to SSRP1, but lacks the HMG chromatin binding domain. Instead, the yFACT complex of Spt16p and Pob3p, binds to nucleosomes where multiple copies of the HMG-domain containing protein Nhp6p have already bound, but Nhp6p does not form a stable complex with the Spt16p/Pob3p heterodimer.

Kevin Struhl, Richard Singer, and Tim Formosa will be cited as definition dbxrefs for their contributions to the discussion. Many thanks to all who participated and helped me understand how to best represent the FACT complex.

-Karen

Original comment by: krchristie

[gocentral]

• status: open --> closed-accepted

Original comment by: krchristie