Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing

• Published in: Genome Biology Vol. 22; no. 1; p. 22
• Main Authors: Gao, Yubang, Liu, Xuqing, Wu, Bizhi, Wang, Huihui, Xi, Feihu, Kohnen, Markus V., Reddy, Anireddy S. N., Gu, Lianfeng
• Format: Journal Article
• Language: English
• Published: London BioMed Central 07.01.2021
• Subjects: Algorithms; Datasets; Enzymes; Gene expression; genome; Immunoprecipitation; Method; methylation; N6-methyladenosine; nanopores; Polyadenylation; Populus trichocarpa; precipitin tests; Ribonucleic acid; RNA; Standard deviation; Transcription; Transcriptomes; Xylem
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-020-02241-7

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.