Technologies for Deciphering Epigenomic DNA Patterns

DNA methylation, consisting on the covalent addition of a methyl group in cytosines, plays a vital role for the development and correct functioning of cells. It constitutes a mechanism by which cell genome is regulated, allowing from a common genome of an individual to obtain all the different cell types that constitute the individual. Nowadays, we understand how the epigenetic machinery works; however, this critical mechanism might promote the appearance of certain diseases if dysregulated, thus the importance of studying the epigenetic patterns on both normal and disease tissues. During the last decades, huge advances on techniques to measure the level of DNA methylation have occurred; we have passed from measuring it with more rudimentary and expensive techniques to nowadays the ability to measure DNA methylation at a single-base resolution in an affordable manner. In this chapter we will cover all the main technologies available, with a special emphasis on the microarray technology, as it supposes a perfect choice taking into account its price as well as the amount of cytosines interrogated, the compatibility with formalin-fixed paraffin-embedded samples, and its standardized procedure.