MIRA-Seq for DNA Methylation Analysis of CpG Islands

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

Financial & competing interests disclosure

This work was supported by NIH grants AG036041, CA160965 and CA084469 awarded to GP Pfeifer. Under a licensing agreement between City of Hope and Active Motif (Carlsbad, CA, USA) the methylated-CpG island recovery assay (MIRA) technique was licensed to Active Motif, and TA Rauch and GP Pfeifer are entitled to (but do not currently receive) a share of the royalties from sales of the licensed technology. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work was supported by NIH grants AG036041, CA160965 and CA084469 awarded to GP Pfeifer. Under a licensing agreement between City of Hope and Active Motif (Carlsbad, CA, USA) the methylated-CpG island recovery assay (MIRA) technique was licensed to Active Motif, and TA Rauch and GP Pfeifer are entitled to (but do not currently receive) a share of the royalties from sales of the licensed technology. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.No writing assistance was utilized in the production of this manuscript.