Recent advances in the analysis of 5-methylcytosine and its oxidation products

DNA methylation (5-methylcytosine, 5-mC) is an important epigenetic mark that has regulatory roles in a broad range of biological processes and diseases. Aberrant DNA methylation is associated with a wide variety of human diseases. Recently, novel cytosine modifications with potential regulatory roles, such as 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and 5-carboxylcytosine (5-caC), were discovered. Systematic investigation of the functions of 5-mC and its oxidation products promotes understanding of the mechanism underlying association of epigenetic modifications with disease biology. In this respect, remarkable advances have been made in developing methods for investigating the occurrence and the localization of these cytosine modifications. In this review, we mainly focus on the recent methodological advances in the analysis of the total levels of 5-mC and its oxidation products (5-hmC, 5-foC and 5-caC). In addition, we summarize and discuss new methods for mapping the genome-wide distribution of 5-hmC, 5-foC and 5-caC.