DNA methylation is an essential mechanism of epigenetic gene regulation with broad relevance in development and disease. Its localization on genomic DNA and general stability make this epigenetic mark an attractive target for large-scale studies in cancer research, developmental biology and ecology. In recent years, microarray-based technologies have been gradually replaced by more robust, accurate and versatile next generation sequencing-based methods.
This presentation will introduce highly-multiplexed reduced representation bisulfite sequencing as a cost-effective means for large DNA methylation studies. The protocol provides a single-base resolution read-out of 5-methylcytosine, while avoiding the cost of whole-genome sequencing. Based on an enzymatic enrichment step, the method is cost-effective, but provides excellent coverage of promoter regions, CpG islands, and other genomic elements such as enhancers and CpG island shores. At the same time, the protocol supports high-throughput applications, is suitable for any vertebrate species and has been optimized specifically for formalin-fixed, paraffin-embedded samples.
In our lab, we have successfully used RRBS on over 2000 samples comprising many different vertebrate species, various cancers, FFPE and low-input samples, and are happy to share our experience with the epigenomics community.