Engineering of a DNA Polymerase for Direct m6A Sequencing

Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6‐methyladenosine (m6A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody‐based enrichment of m6A‐containing RNA prior to sequencing, since m6A modifications are generally “erased” during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6A sequencing. Therefore, we developed a screen to evolve an RT‐active KlenTaq DNA polymerase variant that sets a mark for N6‐methylation. We identified a mutant that exhibits increased misincorporation opposite m6A compared to unmodified A. Application of the generated DNA polymerase in next‐generation sequencing allowed the identification of m6A sites directly from the sequencing data of untreated RNA samples. Deliberate error: A KlenTaq DNA polymerase variant with elevated error rates opposite m6A but not unmodified A in an RNA template was evolved by using a primer‐extension‐based screening assay. The identified mutant was applied in a next‐generation sequencing (NGS) library preparation method and m6A sites could be directly identified in the sequencing data as mutational hotspots.