With single-molecule, real-time (SMRT) sequencing, methylation status of the bases in DNA can be directly identified, as reported online this week in Nature Methods. Being able to determine the methylation profile of a the DNA in cells concurrently with the sequence of their genome will add an extra level of information about how cells are regulated and what goes wrong in disease.
DNA methylation is important in virtually every species; bacteria attach a methyl group to adenosine to regulate their replication and DNA repair, vertebrates use methylation on the cytosine base to regulate gene expression and development. Aberrant DNA methylation is often seen in diseases. Currently scanning for methylated nucleotides relies on indirect detection, which is difficult, time-consuming, and error-prone.
SMRT sequencing by synthesis, developed by Stephen Turner and colleagues, allows for direct detection of methylated nucleotides by recording the kinetics of nucleotide incorporation. The scientists find methylated nucleotides by identifying the longer time interval it takes an enzyme to incorporate the complementary nucleotide during DNA synthesis and apply this to DNA in bacteria.