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 sin...

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Autores principales: Gao, Yubang, Liu, Xuqing, Wu, Bizhi, Wang, Huihui, Xi, Feihu, Kohnen, Markus V., Reddy, Anireddy S. N., Gu, Lianfeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7791831/
https://www.ncbi.nlm.nih.gov/pubmed/33413586
http://dx.doi.org/10.1186/s13059-020-02241-7
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author Gao, Yubang
Liu, Xuqing
Wu, Bizhi
Wang, Huihui
Xi, Feihu
Kohnen, Markus V.
Reddy, Anireddy S. N.
Gu, Lianfeng
author_facet Gao, Yubang
Liu, Xuqing
Wu, Bizhi
Wang, Huihui
Xi, Feihu
Kohnen, Markus V.
Reddy, Anireddy S. N.
Gu, Lianfeng
author_sort Gao, Yubang
collection PubMed
description 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.
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spelling pubmed-77918312021-01-11 Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing Gao, Yubang Liu, Xuqing Wu, Bizhi Wang, Huihui Xi, Feihu Kohnen, Markus V. Reddy, Anireddy S. N. Gu, Lianfeng Genome Biol Method 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. BioMed Central 2021-01-07 /pmc/articles/PMC7791831/ /pubmed/33413586 http://dx.doi.org/10.1186/s13059-020-02241-7 Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Gao, Yubang
Liu, Xuqing
Wu, Bizhi
Wang, Huihui
Xi, Feihu
Kohnen, Markus V.
Reddy, Anireddy S. N.
Gu, Lianfeng
Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
title Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
title_full Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
title_fullStr Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
title_full_unstemmed Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
title_short Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
title_sort quantitative profiling of n(6)-methyladenosine at single-base resolution in stem-differentiating xylem of populus trichocarpa using nanopore direct rna sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7791831/
https://www.ncbi.nlm.nih.gov/pubmed/33413586
http://dx.doi.org/10.1186/s13059-020-02241-7
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