Into the third dimension
Methylation in CpG dinucleotides was clearly insufficient to explain how MeCP2 normally regulates the DLX5 gene. The researchers pursued other possibilities.
To do the actual work of gene suppression, MeCP2 acts in concert with a histone deacetylase protein, HDAC1, and other proteins. Histones are proteins in chromatin equipped with little "tails" that, when attached to an acetyl group (CH3OH), relax to allow the chromatin structure to become open or less compacted. When acetyl groups are not present, the deacetylated chromatin condenses.
Genes are not expressed in silent chromatin because their DNA is tightly constrained by deacetylated histones, which prevents transcription enzymes from accessing the gene. Kohwi-Shigematsu and her team found a discrete deacetylated region of chromatin in the Dlx5/Dlx6 gene neighborhood that coincided with the main MeCP2 binding site.
In MeCP2-knockout mouse brain, this silent chromatin was missing. Kohwi-Shigematsu and her colleagues decided to investigate what effect MeCP2 might have on the structure of chromatin near this site in three dimensions. To this end, they created a complex new assay, the chromatin immunoprecipitation-combined loop assay, and used it to uncover a remarkable arrangement of chromatin loops in the Dlx5/Dlx6 neighborhood.
In wild-type mice, they found that MeCP2 is required for the formation of a loop of silent chromatin between the Dlx5 and Dlx6 genes, by bringing together two sequences separated by more than 10,000 base pairs. This silent chromatin loop configuration could not be formed in MeCP2-null b
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Contact: Paul Preuss
paul_preuss@lbl.gov
510-486-6249
DOE/Lawrence Berkeley National Laboratory
19-Dec-2004