EpiRADseq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing

1. Research addressing the role of epigenetics in a diversity of experimental and natural systems is rapidly accumulating. Diverse methods have been developed to study epigenetic states, including bisulfite sequencing and AFLP-based approaches. However, existing methods are sometimes difficult to apply to non-traditional model organisms that lack genomic resources (bisulfite sequencing), and can fail to be economical and readily scalable to diverse research questions because of reliance on traditional Sanger sequencing (AFLP approaches). 2. Here we develop a reduced-representation library-based approach that is scalable and economical to quantitatively compare patterns of genome-wide methylation. This approach shares substantial similarity to the now widely used double digest restriction-site associated DNA sequencing-based method (ddRADseq), except that it utilizes a methylation-sensitive restriction enzyme. This method therefore identifies changes in the genomic methylation state of c...