Quantitative profiling of N 6 -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; pp. 22 - 17
• 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: England BMC 07.01.2021
• Subjects: Adenosine - analogs & derivatives; Adenosine - genetics; Adenosine - metabolism; Algorithms; Alternative polyadenylation; Base Sequence; Cell Differentiation; Gene Expression Profiling; Immunoprecipitation; N 6-Methyladenosine; Nanopore direct RNA sequencing; Nanopore Sequencing; Nanopores; Polyadenylation; Populus - genetics; Populus - metabolism; Populus trichocarpa; Sequence Analysis, RNA; Stem-differentiating xylem; Transcriptome; Xylem - genetics; Xylem - metabolism; Alternative polyadenylation; Stem-differentiating xylem; Populus trichocarpa; N 6-Methyladenosine; Nanopore direct RNA sequencing
• ISSN: 1474-760X
• DOI: 10.1186/s13059-020-02241-7

There are no comprehensive methods to identify N -methyladenosine (m A) at single-base resolution for every single transcript, which is necessary for the estimation of m A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m 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 A-sensitive RNA-endoribonuclease-facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m A.