Journal Article

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

Reddy, Anireddy S. N., Kohnen, Markus V., Gu, Lianfeng, Xi, Feihu, Gao, Yubang, Liu, Xuqing, Wu, Bizhi, Wang, Huihui

2021

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V
• Subject: Algorithms / Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Datasets / Enzymes / Evolutionary Biology / Gene expression / genome / Human Genetics / Immunoprecipitation / Life Sciences / Method / methylation / Microbial Genetics and Genomics / N6-methyladenosine / nanopores / Plant Genetics and Genomics / Polyadenylation / Populus trichocarpa / precipitin tests / Ribonucleic acid / RNA / Standard deviation / Transcription / Transcriptomes / Xylem