Drs. Urich, Nery and Ecker from the The Salk Institute for Biological Studies, along with Lister from the University of Western Australia and Schmitz from the University of Georgia, Athens published a new protocol for MethylC-Seq in Nature Protocols in conjunction with the Nature publication, Integrative analysis of 111 reference human epigenomes, which unveiled the map of the epigenome funded by the NIH Roadmap Epigenomics Program.
Their MethylC-Seq protocol allows for the identification of DNA methylation features which are not readily apparent from traditional bisulfite-PCR methods, such as the identification of non-CG methylation in human embryonic stem cells and brain tissues, and the identification of large partially methylated domains in animal genomes. By incorporating the NEXTflex™ Bisulfite-Seq Barcodes, cytosine-methylated universal adapters, into the protocol, the need for targeted primer design is eliminated, thereby eliminating associated biases.
This MethylC-Seq protocol can be used to determine the inheritance of DNA methylation states, revealing the spontaneous epimutation rate for single-methylation polymorphisms (SMPs), the prevalence of spontaneous epialleles and widespread evidence for population-wide association of genetic variants (methylQTL) with methylation variants. This protocol can also been applied to understand the patterns of DNA methylation throughout development, between species, within hybrids and between mutants.
Urich, M. A., Nery, J. R., Lister, R., Schmitz, R. J. and Ecker, J. R. (2015) MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols 10, 475–483. doi:10.1038/nprot.2014.114.