Small Molecules Targeting H3K9 Methylation Prevent Silencing of Reactivated Alleles in Fragile X Syndrome Patient Derived Cells

In fragile X syndrome (FXS), expansion of a CGG repeat tract in the 5'-untranslated region of the gene to >200 repeats causes transcriptional silencing by inducing heterochromatin formation. Understanding the mechanism of silencing is important as gene reactivation is a potential treatment approach for FXS. To date, only the DNA demethylating drug 5-azadeoxycytidine (AZA) has proved effective at gene reactivation; however, this drug is toxic. The repressive H3K9 methylation mark is enriched on the gene in FXS patient cells and is thus a potential druggable target. However, its contribution to the silencing process is unclear. Here, we studied the effect of small molecule inhibitors of H3K9 methylation on expression in FXS patient cells. Chaetocin showed a small effect on gene reactivation and a synergistic effect on mRNA levels when used in combination with AZA. Additionally, chaetocin, BIX01294 and 3-Deazaneplanocin A (DZNep) were able to significantly delay the re-silencing of AZA-reactivated alleles. These data are consistent with the idea that H3K9 methylation precedes DNA methylation and that removal of DNA methylation is necessary to see the optimal effect of histone methyl-transferase (HMT) inhibitors on gene expression. Nonetheless, our data also show that drugs targeting repressive H3K9 methylation marks are able to produce sustained reactivation of the gene after a single dose of AZA.