Genome-Wide DNA Methylation and RNA Expression Differences Correlate with Invasiveness in Melanoma Cell Lines

Abstract

<b>Aims & objectives:</b> The aim of this study was to investigate the role of DNA methylation in invasiveness in melanoma cells. <b>Materials & methods</b>: The authors carried out genome-wide transcriptome (RNA sequencing) and reduced representation bisulfite sequencing methylome profiling between noninvasive (n = 4) and invasive melanoma cell lines (n = 5). <b>Results:</b> The integration of differentially expressed genes and differentially methylated fragments (DMFs) identified 12 DMFs (two in <i>AVPI1</i>, one in <i>HMG20B</i>, two in <i>BCL3</i>, one in <i>NTSR1</i>, one in <i>SYNJ2</i>, one in <i>ROBO2</i> and four in <i>HORMAD2</i>) that overlapped with either differentially expressed genes (eight DMFs and six genes) or cis-targets of lncRNAs (five DMFs associated with cis-targets and four differentially expressed lncRNAs). <b>Conclusions:</b> DNA methylation changes are associated with a number of transcriptional differences observed in noninvasive and invasive phenotypes in melanoma.