GSE169695
DNA methylation analysis by DREAM of UV irradiated melanocytes
Ultraviolet radiation (UVR) is the greatest risk factor for melanoma development. While the role of UVR in DNA mutagenesis is generally accepted, the role of UVR-induced mutations in melanomagenesis remains controversial.  To understand better how UVR is contributing to melanoma development, we investigated the non-mutational effect of UVR on the epigenome, specifically DNA methylation.  Aberrant DNA methylation changes are a hallmark in melanoma and there are few reports on the effects of UVR on DNA methylation. We exposed melanocytes to UVR and cultured them for one-month to detect heritable and stable changes in DNA methylation. We found both hyper and hypo methylated sites after UVR exposure. While many of these changes occurred outside of promoters and areas of active gene expression, there were changes in promoter DNA methylation changes that correlated with changes in gene expression.  These changes also correlated with those found in melanoma and UVR sensitive sites were prognostic of patient overall survival. Our work shows  UVR-induced DNA methylation changes in melanocytes and may be a novel non-mutational mechanism in which UVR contributes to melanoma development. Overall design: Melanocyte cells were UV irradiated with a broad spectrum wave band ( UVA & UVB) for a total dos of 175 J/m2. Cells were cultured for one month before performing digital restriction enzyme analysis of methylation (DREAM). Genomic DNA was digested by SmaI which recognizes unmethylated CpG sites in the sequence CCCGGG and cuts leaving a 5'-GGG signature. Next, digestion by XmaI was performed which can cut methylated CpG sites in the sequence CCCGGG and leaves a 5'-CCGGG signature. High throughput sequencing was used to map these sites to the genome. Methylation ratios were calculated as the total number of XmaI signature reads over the total number of reads for each specific site. Methylation ratios were adjusted for differences in restriction enzyme efficiency based on values from spiked in methylation standards.