Next generation sequencing allows researchers to generate high resolution maps of epigenetic modifications for whole genomes (epigenome). Whole genome methylation pattern has been determined e.g. for A. thaliana by sequencing bisulfite treated DNA with Illumina technology (Lister et al., 2008 and Cokus et al., 2008).
In the near future epigenetic studies may be possible without bisulfite treatment by single-molecule real-time sequencing (SMRT). The first proof of concept study promises direct detection of modified nucleotides as well as discrimination between different types of modifications (Flusberg et al., 2010).