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

Genome Biol. 2021 Jan 7;22(1):22. doi: 10.1186/s13059-020-02241-7.

Abstract

There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m6A 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 m6A-sensitive RNA-endoribonuclease-facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m6A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m6A.

Keywords: Alternative polyadenylation; N 6-Methyladenosine; Nanopore direct RNA sequencing; Populus trichocarpa; Stem-differentiating xylem.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / analogs & derivatives*
  • Adenosine / genetics
  • Adenosine / metabolism*
  • Algorithms
  • Base Sequence
  • Cell Differentiation
  • Gene Expression Profiling
  • Immunoprecipitation
  • Nanopore Sequencing*
  • Nanopores*
  • Polyadenylation
  • Populus / genetics
  • Populus / metabolism*
  • Sequence Analysis, RNA*
  • Transcriptome
  • Xylem / genetics
  • Xylem / metabolism*

Substances

  • N-methyladenosine
  • Adenosine