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

MIRA-seq for DNA methylation analysis of CpG islands.

Author information

1
Beckman Research Institute, City of Hope, Duarte, CA 91010, USA.
2
Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA.
3
Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Abstract

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

PMID:
25881900
PMCID:
PMC4607651
DOI:
10.2217/epi.15.33
[Indexed for MEDLINE]
Free PMC Article

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