I'm studying a gene whose expression is regulated by DNA methylation. Cancer cell lines that express this gene show strong hypomethylation, while cells lines that don't express it show hypermethylation. It's also from a family of genes (LY6 family) that are nearly all regulated by DNA methylation. I've confirmed this methylation profile with bisulfite sequencing.

In cells that don't normally express it (hypermethylated cells), I see a strong (~20 fold) increase in expression following radiation treatment. I hypothesized that this was due to changes in methylation. But when I did bisulfite sequencing on irradiated cells, I see that they are still methylated.

Is there any mechanism (besides methylation) that can explain this? I'd really appreciate any help! Thanks!