The Methylation Toolkit: What's new in Epigenomic Engineering?

A potent method for identifying 5-methylcytosine in DNA, bisulfite sequencing has greatly advanced our knowledge of epigenetic control in both plants and animals.In the meanwhile, studies on further base alterations, such as 6-methyladenine and 4-methylcytosine, which are common in prokaryotes, has been hindered by the absence of a similar method. DNA degradation, lack of selectivity, and short reads with poor sequence diversity are just a few of the challenges that bisulfite sequencing faces. In this study, we examine the latest developments in bisulfite sequencing techniques that allow mapping single-cell methylomes, identifying derivatives of 5-methylcytosine, and focusing on genomic regions of interest. The special benefit of long-read sequencing in identifying base changes in native DNA is then discussed, along with the advantages and disadvantages of PacBio and Nanopore sequencing for this use. The capacity to identify different modified bases from a universal sample preparation, along with the mapping and phasing benefits of the longer read lengths, give long-read sequencing a clear advantage over short-read bisulfite sequencing for an increasing number of applications across kingdoms, even though analyzing epigenetic data from long-read platforms is still difficult.