Useful methods to study epigenetic marks: DNA methylation, histone modifications, chromatin structure, and noncoding RNAs

Epigenetics refers to the study of reversible and inheritable information that regulates gene expression and genome stability beyond that contained in the DNA sequence. Epigenetic mechanisms include DNA methylation, posttranslational modifications (PTMs) in histones, and noncoding RNAs (ncRNAs). Different approaches have been developed to study DNA methylation both at a global level and at genome-specific regions. Furthermore, some methodologies allow quantifying the global content of PTMs in histones, as well as their interactions with proteins and location along the genome. Regarding chromatin, it is possible to define its accessibility, interaction with proteins and RNA, and conformation. For ncRNAs, the approaches are directed to their expression, location, and interaction with DNA, RNA, and proteins. Thus, several methodologies have allowed a better understanding of the role of epigenetic marks in different conditions, including DNA damage and repair, which are discussed in this chapter.