Global DNA methylation level sensing using methyl-CpG binding domain-fused luciferase and fluorescent protein

Abstract

Methylation at the 5-position of cytosine in CpG dinucleotides is involved in the regulation of gene expression. In cancer cells, aberrant CpG methylation patterns are observed, characterized by promoter hypermethylation on tumor suppressor genes and global hypomethylation inducing genomic instability. We previously reported that global DNA methylation levels were quantified by bioluminescence resonance energy transfer (BRET) between methyl-CpG binding domain (MBD)-fused firefly luciferase and DNA intercalating dye. The assay simply and accurately detects global DNA methylation levels, but requires a 30-min incubation period for the DNA intercalating dye to bind to genomic DNA. In this study, a rapid system for measuring global DNA methylation levels was developed using MBD-fused NanoLuc luciferase (Nluc) and MBD-fused fluorescent protein, monomeric Venus (mVenus). When the MBD-fused Nluc and MBD-fused mVenus simultaneously bind to adjacent methyl-CpGs, the amount of which is associated with the global DNA methylation level, BRET occurs between two. We demonstrated that the BRET signal between MBD-fused Nluc and MBD-fused mVenus was detected on double-stranded DNA containing two methyl-CpG sites, and the efficiency depended on the distance between two methyl-CpG sites. In addition, global DNA methylation levels were quantified within 3 min by the BRET assay (R² = 0.99). These results indicate that the global DNA methylation levels can be easily, accurately, and rapidly quantified by the BRET assay using MBD-fused Nluc and MBD-fused mVenus.