Computational Analysis of Epigenetic Modifications in Melanoma

Cancer cells utilize genetic and epigenetic aberrations to drive excessive proliferation. Although our understanding of genetic alterations has drastically increased, we have limited understanding of epigenomic features of cancer. In this chapter, we focus on the most aggressive skin cancer-cutaneous melanoma-and present the progress made in our understanding of epigenome of melanoma tumors. We first describe the current knowledge on epigenetic features of melanoma cells discovered using classical methods and more recent sequencing-based methodologies. We present the concepts, the methodologies, and computational analysis of epigenomic methods that are currently being utilized for defining epigenomic aberrations in melanoma. We focus on most popular methods such as RRBS for DNA methylation analyses, ChIP-Seq for histone modification and transcription factor binding, ATAC-Seq for chromatin accessibility and nucleosome positioning, and Hi-C for higher-order chromatin structure determination. Finally, we provide perspective on future studies needed to comprehensively define melanoma epigenome.