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Gene Expression Goes Loopy for Mediator and Cohesin

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By Stuart P. Atkinson

DNA looping to allow proximity of enhancers and promoter sequences has been suggested as a means to regulate gene expression, but the mechanisms by which this occurs and the factors involved are still to be fully understood. However an advance online publication from Nature uncovers a mechanism by which DNA-looping-mediated regulation of gene expression occurs in mouse embryonic stem cells (mESC).

While studying genes required for the regulation of transcription and chromatin needed for the pluripotency of mESC, Kagey and colleagues from the laboratory of Richard A. Young, found that a large number of components of the Mediator and Cohesin complexes and the Cohesin loading factor Nipbl were required for the maintenance of an ESC like state. Mediator is known as a transcriptional co-activator while Cohesin is thought to play a role in gene expression and chromosome segregation. It was subsequently found that both the Mediator and Cohesin complexes co-occupied enhancer regions and promoter regions of active genes, such as Oct4, in mESC. Interestingly, Nipbl seemed to be specifically found at regions co-occupied by Mediator and Cohesin, but not regions co-occupied by Cohesin and Ctcf, another interaction thought to play a role in gene loop formation and gene regulation (Wendt et al.and Hadjur et al.). Further, siRNA mediated gene down-regulation of Nipbl and members of the Mediator and Cohesin complexes, indicated that of the 2,700 genes co-occupied by Mediator, Cohesin and Nipbl in mESC, 700 showed significant changes in expression upon siRNA mediated down-regulation, suggesting that a subset of active genes in mESC require Cohesin, Mediator and Nipbl. Physical interaction of Mediator, Cohesin and Nipbl was then demonstrated by various immunoprecipitation assays, while chromosome conformation capture (3C) demonstrated the formation of DNA loops between enhancers and promoters of genes that are active in ESC and are know to have Mediator, Cohesin and Nipbl bound at their regulatory regions (Nanog, Phc1, Oct4 and Lefty1). Interestingly, this was not observed in mouse embryonic fibroblasts (MEFs) in which each of the genes tested is not expressed, indicating a role for Mediator, Cohesin and Nipbl in the formation of cell-type-specific chromatin structure.

 

This paper represents another step forward in our understanding of how the pluripotent nature of ESCs is maintained and also our understanding of basic gene regulation. Further this also allows us to further understand many human developmental syndromes associated with mutations in the genes investigated within this study. Various syndromes are associated with Mediator gene mutations (Risheg, H. et al., Schwartz, C. E. et al. and Ding, N. et al.) and mutations in Nipbl are associated with Cornelia de Lange syndrome (Strachan, T.), characterised by developmental defects and mental retardation and is linked to deregulation of gene expression. This study therefore suggests that mutations in such genes may play a role in the dysregulation of gene expression due to defects in gene looping.

References

Kagey MH et al.
Mediator and Cohesin connect gene expression and chromatin architecture
Nature, Published online18 August 2010

Wendt, K. S. et al.
Cohesin mediates transcriptional insulation by CCCTC-binding factor.
Nature 451, 796–801 (2008)

Hadjur, S. et al.
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.
Nature 460, 410–413 (2009)

Risheg, H. et al.
A recurrent mutation in MED12 leading to R961W causes Opitz-Kaveggia syndrome.
Nature Genet. 39, 451–453 (2007)

Schwartz, C. E. et al.
The original Lujan syndrome family has a novel missense mutation (p.N1007S) in the MED12 gene.
J. Med. Genet. 44, 472–477 (2007)

Ding, N. et al.
Mediator links epigenetic silencing of neuronal gene expression with x-linked mental retardation.
Mol. Cell 31, 347–359 (2008)

Strachan, T.
Cornelia de Lange Syndrome and the link between chromosomal function, DNA repair and developmental gene regulation.
Curr. Opin. Genet. Dev. 15, 258–264 (2005)