Figure 5. Association of MSat10 copy number with neighboring gene expression and epigenetic marks.

(a) MSat10 is a 5.2 kb GC-rich tandem repeat that lies ∼4 kb distal to the gene ZFP37. Although 6 copies of this 5.2 kb repeat are present in the hg18 assembly this macrosatellite is highly polymorphic in size, varying from 4–42 copies in HapMap. ChIP-seq analysis shows the presence of histone marks characteristic of heterochromatin, such as trimethylation of histone H3 at lysine 9 and trimethylation of histone H4 at lysine 9. Screenshot from the UCSC Genome Browser shows ZFP37 (Zinc Finger Protein 37), the adjacent MSat10 repeat (red arrows), and the results of ChIP-seq analysis. (b) In 58 unrelated CEU HapMap individuals we observed an inverse correlation between copy number of the MSat10 repeat and expression level of the adjacent gene ZFP37, demonstrating suppression of ZFP37 expression associated with larger repeat sizes (c) Using a targeted Sequenom assay, we confirm that variable methylation of MSat10 is highly correlated with repeat number (R² = 0.76, p = 4.4×10⁻¹²), showing a strong relationship between repeat size and local epigenetic state. (d) Proposed model of repeat induced gene silencing at the MSat10 locus. At low repeat numbers the region is euchromatic and the expression of the neighboring ZFP37 gene is high. However, expansions of the macrosatellite result in an accumulation of heterochromatic marks in the region, including repressive histone modifications and DNA methylation, resulting in the suppression of local gene expression. Although our model shows methylation on all MSat10 copies, our data does not exclude the possibility that on expanded MSat10 alleles DNA methylation is limited to a subset of the repeat units. Lollipops represent DNA methylation, with open circles being low and filled black circles high DNA methylation, and grey ‘Me’ bubbles represent repressive histone methylation.