Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq

Abstract

Abstract DNA N6-methyladenine (6mA) is prokaryotes' most prevalent type of DNA methylation. Recently, 6mA has been identified in eukaryotic genomes, but the prevalence of 6mA in eukaryotes has been debated due to the limitations of current 6mA genomic profiling and quantification methods. To solve the challenges, we develop a chemical-based sequencing method, Nitrite-assisted Amino MEthylation sequencing (NAME-seq), for genomic profiling and single-base quantification of DNA N6-adenine methylation rate. NAME-seq combines nitrite conversion of 6mA to nitrosylated-6mA (6mA-NO) with Klenow fragment (3'→5' exo−) mediated DNA synthesis to induce the 6mA-to-T transversion specifically. We apply NAME-seq to bacterial and eukaryotic genomes; NAME-seq can accurately map 6mA and quantify the ratio at single-base resolution. Moreover, we show that NAME-seq can be applied with 6mA-MeDIP-seq to map 6mA in the human genome and improve accuracy. In summary, NAME-seq is an efficient method for quantitative 6mA mapping at single-base resolution.