AIM: To develop a reliable method for whole genome analysis of DNA methylation.
MATERIALS & METHODS: Genome-scale analysis of DNA methylation includes 
affinity-based approaches such as enrichment using methyl-CpG-binding proteins. 
One of these methods, the methylated-CpG island recovery assay (MIRA), is based 
on the high affinity of the MBD2b-MBD3L1 complex for CpG-methylated DNA. Here we 
provide a detailed description of MIRA and combine it with next generation 
sequencing platforms (MIRA-seq).
RESULTS: We assessed the performance of MIRA-seq and compared the data with 
whole genome bisulfite sequencing.
CONCLUSION: MIRA-seq is a reliable, genome-scale DNA methylation analysis 
platform for scoring DNA methylation differences at CpG-rich genomic regions. 
The method is not limited by primer or probe design and is cost effective.