Alternative Methods

Bisulfite Sequencing Methods

Although the use of whole genome bisulfite sequencing to analyse DNA methylation in CG, CHG, and CHH context is highly relevant to the study of epigenetics in plant ecology, it is not all-encompassing. There are indeed other techniques based on similar principles that can be used to capture methylation information, such as methylated DNA immunoprecipitation (meDIP) which can be used in combination with high-resolution DNA microarrays or high-throughput next-generation sequencing.

Recently there has also been some investigation into treatments that can facilitate nucleotide-level base conversion without the harsh side effects of sodium bisulfite [Yibin et al. 2019]. The advent of long-read sequencing technologies such as single molecule real-time (SMRT) analysis with PacBio or Nanopore has also provided an alternative to bisulfite sequencing. The base calling in these approaches can provide wavelength profiles for each nucleotide that differ between bases with and without base modifications [Flusberg et al. 2010]. This has the advantage of detecting DNA methylation without the need for harsh bisulfite treatment, while also allowing for detection of other forms of base modification. Unfortunately the profiles can be difficult to differentiate, but development of machine learning techniques may be a promising avenue of advancement in this regard.