MIRA

MIRA

(MIRA) uses the high affinity of a methylated-CpG-binding protein complex (MBD2B and MBD3L1) to enrich regions with methylated CpG dinucleotides. This approach can be applied to both array-based DNA analysis and NGS sequencing, which are sometimes distinguished as MIRA-chip and MIRA-Seq.

In the MIRA procedure, the fragmented genomic DNA is incubated with purified GST-MBD2B and His-MBD3L1 proteins. The high affinity MBD2B/MBD3L1 complex binds to the methylated genomic DNA templates. The methylated genomic DNA fragments are captured on glutathione-coated magnetic beads. The enriched methylated DNA fraction is amplified, labeled and analyzed by NGS sequencing.

Pros:

• High specificity and sensitivity requiring as little as 1ng input gDNA
• Does not require DNA denaturation
• Independent of restriction sites

Cons:

• Resolution limited to 100 bases
• It requires a minimum of two methylated CpGs in the captured fragment¹

• MIRA: Rauch T. A. and Pfeifer G. P. (2010) DNA methylation profiling using the methylated-CpG island recovery assay (MIRA). Methods 52: 213-217
• MIRA-ChIP: Jung M., Jin S. G., Zhang X., Xiong W., Gogoshin G., et al. (2015) Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging. Nucleic Acids Res
• MIRA-Seq: Benjamin A. L., Green B. B., Crooker B. A., McKay S. D. and Kerr D. E. (2016) Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome. BMC Genomics 17: 258
• 1. Rauch T. A. and Pfeifer G. P. (2011) Methods for Assessing Genome-wide DNA Methylation. 135-147

1. Benjamin A. L., Green B. B., Crooker B. A., McKay S. D. and Kerr D. E. (2016) Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome. BMC Genomics 17: 258
2. Jin S. G., Xiong W., Wu X., Yang L. and Pfeifer G. P. (2015) The DNA methylation landscape of human melanoma. Genomics 106: 322-330