placement of Transcription cofactor activity

[gocentral]

Hi

the UK curators are not convinced that GO:0003714 transcription corepressor activity should be a child of GO:0003712 Transcription cofactor activity. The jamboree gene NIPBL is considered a transcription corepressor; but there is no evidence that this activity is via transcription factor binding. Its effect is through the regulation of the amount of histone deacetylation in the promoter region. Therefore we would like to see this relationship removed.

Thanks

Ruth

Reported by: RLovering

Original Ticket: geneontology/ontology-requests/7076

[gocentral]

Karen is already planning to review the definitions of transcription cofactor, coactivator, and corepressor as part of a general overhaul she's working on, so I'll assign this to her. Wiki:

http://wiki.geneontology.org/index.php/Transcription

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> kchris

Original comment by: mah11

[gocentral]

• labels: 397373 --> transcription
• status: open --> closed-out-of-date

Original comment by: paolaroncaglia

[gocentral]

• status: closed-out-of-date --> pending-out-of-date

Original comment by: rebeccafoulger

[gocentral]

• status: pending-out-of-date --> open

Original comment by: krchristie

[gocentral]

• status: open --> closed-later

Original comment by: paolaroncaglia

[gocentral]

Hi Karen,

Would you have any comments on this?

Thanks, Jane, Becky, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: closed-later --> open-later

Original comment by: paolaroncaglia

[gocentral]

Hi Ruth,

Perhaps you could provide a paper where NIPBL is referred to as a transcription corepressor. I just searched for "NIPBL" and out of 78 citations, only three mention "transcription" in the title, listed below.

1: Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D. Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma. 2008 Feb;117(1):89-102. Epub 2007 Oct 27. PubMed PMID: 17965872; PubMed Central PMCID: PMC2258211.

2: Kawauchi S, Calof AL, Santos R, Lopez-Burks ME, Young CM, Hoang MP, Chua A, Lao T, Lechner MS, Daniel JA, Nussenzweig A, Kitzes L, Yokomori K, Hallgrimsson B, Lander AD. Multiple organ system defects and transcriptional dysregulation in the Nipbl(+/-) mouse, a model of Cornelia de Lange Syndrome. PLoS Genet. 2009 Sep;5(9):e1000650. Epub 2009 Sep 18. PubMed PMID: 19763162; PubMed Central PMCID: PMC2730539.

3: Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Clark D, Kaur M, Tandy S, Kondoh T, Rappaport E, Spinner NB, Vega H, Jackson LG, Shirahige K, Krantz ID. Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol. 2009 May 5;7(5):e1000119. Epub 2009 May 26. PubMed PMID: 19468298; PubMed Central PMCID: PMC2680332.

Looking at the abstracts of these 3 papers suggests that NIPBL is a regulator of cohesin loading onto chromatin. Looking specifically at the Liu et al paper, they clearly state that they think that cohesin binds in promoter regions and may play a role as a transcription factor, for example:

"To summarize, in control LCLs cohesin preferentially binds to transcribed genes at the TSSs as compared to the silent nontranscribed genes. The binding sites are even more enriched for the differentially expressed genes. In CdLS, cells tend to lose cohesin binding globally, however the cohesin sites at TSSs are more likely to be lost, most notably for the differentially expressed genes where loss of cohesin binding at the TSSs results in a binding frequency approaching the background level. The preferential binding to promoter regions suggests cohesin may play a role as a transcription factor."

However, nowhere in this paper do they use the word "cofactor" or "corepressor". If I search in PubMed for "NIPBL AND corepressor", I get 0 hits.

So, I am really unclear as to the basis of the statement you've made that NIPBL is considered a transcription corepressor. If you could provide appropriate citations, I'll take a look.

-Karen

Original comment by: krchristie

[gocentral]

Hi,

In the absence of some indication as to why NIPBL should be considered a transcription corepressor, I am going to close this item.

-Karen

Original comment by: krchristie

[gocentral]

• status: open-later --> closed-later

Original comment by: krchristie

[gocentral]

• status: closed-later --> closed-invalid

Original comment by: krchristie