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

DNA N6-methyladenine (6mA) is the most widespread type of DNA methylation in prokaryotes. However, the prevalence of 6mA in eukaryotes has recently been challenged due to the limitations of current 6mA detection techniques. Here, we present a chemical-based sequencing method, Nitrite-assisted Amino MEthylation sequencing (NAME-seq), for quantitative, whole-genome mapping of 6mA at single-base resolution. NAME-seq combines nitrite conversion of 6mA to nitrosylated-6mA (6mA-NO) with Klenow Fragment (3'?5' exo-) random priming to induce a 6mA-to-T transversion specifically. We apply NAME-seq to two bacterial species and show that, compared to SMRT-seq, NAME-seq results in a more specific and robust detection of 6mA. NAME-seq can also accurately map 6mA in the C. reinhardtii genome at single-base resolution. Additionally, we show that NAME-seq can be combined with conventional DIP-seq to detect 6mA in the Dam-methylated human genome with high specificity. Therefore, we further perform DIP-NAME-seq to profile 6mA in WT and TASOR KO K562 cell line and revealed that 6mA is enriched at specific motifs (HYYHAG and CACACA) and H3K9me3 regions. In summary, we demonstrate NAME-seq is a specific and sensitive sequencing method for quantitative 6mA mapping at single base resolution across different model organisms. Overall design: NAME-seq to native genomic DNA without any enrichment