مقایسه تکنیک های آنالیز گسترده ژنوم به آنالیز متیلاسیون DNA Comparison of genome-wide analysis techniques to DNA methylation analysis in human cancer

1. Introduction DNA methylation as an epigenetic alteration commonly occurs at 5′cytosine (5′C) of pyrimidine cycle and plays a key role in genome regulation and development [1-3]. Apart from its role in physiological functions, aberrant DNA methylation is related to the inappropriate transcriptional silencing of genes [4, 5], that provides an advantage for several diseases such as diabetes, heart disease, autoimmune and aging-related diseases [6-10] and many types of cancer including colorectal [11-13], lung [14, 15], liver [16, 17], and breast cancer [18]. In contrast to normal cells, cancer cells globally exhibit a lower levels of 5-methylcytosine in the genome, but simultaneously a higher levels of methylation in tumor suppressor genes promoters [19, 20]. DNA methylation can silence the expression of tumor suppressor genes through mechanisms that may interfere with transcription factor binding sites or through conformational changes in chromatin structure leading to transcriptionally silencing [21-23]. Therefore, it is important to know how DNA methylation patterns changes during physiological development and pathological disorders. Given the important role of DNA methylation in the biological phenomena, a close examination of DNA methylation status can be applied to identify tumor markers and therapeutic targets in cancer patients [19, 24]. Moreover, reversible epigenetic modifications can be considered as more effective targets for therapeutic purposes than irreversible genetic mutations. Silenced genes with DNA methylation or histone deacetylation can be restored to normal functioning through epigenetic inhibitors [6, 25, 26]. An accurate determination of methylation patterns is required to clarify their pivotal roles in biological processes. Therefore, better understanding of each methylation detection method and its application would be important to select appropriate effective system to evaluate methylation status. There are a growing number of methylation assays which is commonly applied for the evaluation of DNA methylation. In this review we generally describe three kinds of common approaches to profiling genome-wide DNA methylation; i) restriction enzyme-based techniques, ii) affinity enrichment-based techniques, iii) bisulfite conversion-based methods and explain the main advantages and drawbacks of these techniques (Table 1).