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How Do You Identify m⁶ A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets

Capitanchik, C; Toolan-Kerr, P; Luscombe, NM; Ule, J; (2020) How Do You Identify m⁶ A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets. Frontiers in Genetics , 11 , Article 398. 10.3389/fgene.2020.00398. Green open access

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Abstract

A flurry of methods has been developed in recent years to identify N6-methyladenosine (m6A) sites across transcriptomes at high resolution. This raises the need to understand both the common features and those that are unique to each method. Here, we complement the analyses presented in the original papers by reviewing their various technical aspects and comparing the overlap between m6A-methylated messenger RNAs (mRNAs) identified by each. Specifically, we examine eight different methods that identify m6A sites in human cells with high resolution: two antibody-based crosslinking and immunoprecipitation (CLIP) approaches, two using endoribonuclease MazF, one based on deamination, two using Nanopore direct RNA sequencing, and finally, one based on computational predictions. We contrast the respective datasets and discuss the challenges in interpreting the overlap between them, including a prominent expression bias in detected genes. This overview will help guide researchers in making informed choices about using the available data and assist with the design of future experiments to expand our understanding of m6A and its regulation.

Type: Article
Title: How Do You Identify m⁶ A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets
Location: Switzerland
Open access status: An open access version is available from UCL Discovery
DOI: 10.3389/fgene.2020.00398
Publisher version: https://doi.org/10.3389/fgene.2020.00398
Language: English
Additional information: Copyright © 2020 Capitanchik, Toolan-Kerr, Luscombe and Ule. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) (http://creativecommons.org/licenses/by/4.0/). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Keywords: RNA, N6-methyladenosine, m6A, epitranscriptomics, bioinformatics
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10101489
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