MIRA-seq for DNA methylation analysis of CpG islands

Epigenomics. 2015 Aug;7(5):695-706. doi: 10.2217/epi.15.33. Epub 2015 Apr 17.


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.

Keywords: CpG islands; DNA methylation; high-throughput sequencing; methyl-CpG-binding protein; methylated-CpG island recovery assay.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cell Line
  • CpG Islands / genetics*
  • DNA Methylation*
  • Epigenomics / methods*
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Genome, Human / genetics
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Models, Genetic
  • Reproducibility of Results