Enzymatic, Nondestructive Sequencing of 5-Methylcytosine with Direct Methylation Sequencing (DM-Seq)

Here, we provide a detailed protocol for Direct Methylation Sequencing (DM-Seq), a method for localizing 5-methylcytosine (5mC) at single-base resolution within CpG contexts. DM-Seq relies solely on enzymatic transformation of DNA, thereby circumventing the generation of destructive or biased intermediates commonly seen with chemical sequencing methods, and provides results with high library yield, sample diversity, and fidelity. DM-Seq is particularly well-suited for low-input samples and applications where the detection of 5mC is desired without being confounded by 5-hydroxymethylcytosine. In this chapter, we present a comprehensive workflow for the entire method, from the synthesis and purification of the requisite substrates and enzymes to the construction and analysis of the sequencing library.