Accurate detection of m6A RNA modifications in native RNA sequences

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  • dc.contributor.author Liu, Huanle
  • dc.contributor.author Begik, Oguzhan
  • dc.contributor.author Lucas, Morghan C.
  • dc.contributor.author Ramirez, Jose Miguel
  • dc.contributor.author Mason, Christopher E.
  • dc.contributor.author Wiener, David
  • dc.contributor.author Schwartz, Schraga
  • dc.contributor.author Mattick, John S.
  • dc.contributor.author Smith, Martin A.
  • dc.contributor.author Novoa, Eva Maria
  • dc.date.accessioned 2020-04-01T08:42:52Z
  • dc.date.available 2020-04-01T08:42:52Z
  • dc.date.issued 2019
  • dc.description.abstract The epitranscriptomics field has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here, we show that using direct RNA sequencing, N6-methyladenosine (m6A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. Specifically, we find that our algorithm, trained with m6A-modified and unmodified synthetic sequences, can predict m6A RNA modifications with ~90% accuracy. We then extend our findings to yeast data sets, finding that our method can identify m6A RNA modifications in vivo with an accuracy of 87%. Moreover, we further validate our method by showing that these 'errors' are typically not observed in yeast ime4-knockout strains, which lack m6A modifications. Our results open avenues to investigate the biological roles of RNA modifications in their native RNA context.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Liu H, Begik O, Lucas MC, Ramirez JM, Mason CE, Wiener D, Schwartz S, Mattick JS, Smith MA, Novoa EM. Accurate detection of m6A RNA modifications in native RNA sequences. Nat Commun. 2019; 10(1):4079. DOI: 10.1038/s41467-019-11713-9
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-019-11713-9
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/44134
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Commun. 2019; 10(1):4079
  • dc.rights © The Author(s) 2019. Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword RNA modification
  • dc.subject.keyword Software
  • dc.title Accurate detection of m6A RNA modifications in native RNA sequences
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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