Now that we’ve landed smack dab in the middle of the age of big data, some interesting techniques have emerged to interrogate the mind-boggling amounts of information from our (epi)genome. Dr. Ranjan Perera and team at the Sanford-Burnham Medical Research Institute (Florida) applied some of that new analysis wizardry to learn more about the complexity of melanoma by determining “genome-wide methylated CpG island distributions by next-generation sequencing.” Perera shares that this “Analysis revealed that a number of genes that exhibit differential methylation patterns in melanoma cells, at their 5′ regulatory regions, including noncoding RNA genes, can be related to a cancer-related gene network.”
Here’s what the team found:
- “Melanoma chromosomes tend to be differentially methylated over short CpG island tracts” and provide a promising mechanism.
- “CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes…exhibit extensive hypermethylation (as exemplified by “TERC, which encodes the telomerase RNA”)
- However “several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines”, which ultimately highlights the heterogeneity of methylation alterations in cancer.
Perera also shared surprise that “Different LTR elements exhibit different patterns of methylation in their associated CpG islands” and is left wondering: “Are these LTR elements dynamic? Are they moving around in melanoma cells?” Ultimately, Perera concludes, “Genome-wide analysis of epigenetic signatures of cancer cells, when coupled with network-instructed systems biology analysis, can rapidly provide gene candidates for biomarker development.”
Check it out over at Nature’s Scientific Reports, November 2013