Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing

There are no comprehensive methods to identify N(6)-methyladenosine (m(6)A) at single-base resolution for every single transcript, which is necessary for the estimation of m(6)A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m(6)A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m(6)A-sensitive RNA-endoribonuclease–facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m(6)A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m(6)A. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-020-02241-7.