Publications

Publications Search

Search for publications by author
Search for publications by abstract keyword(s)

Accurate detection of m(6)A RNA modifications in native RNA sequences

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, N(6)-methyladenosine (m(6)A) 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 m(6)A-modified and unmodified synthetic sequences, can predict m(6)A RNA modifications with ~90% accuracy. We then extend our findings to yeast data sets, finding that our method can identify m(6)A 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 m(6)A modifications. Our results open avenues to investigate the biological roles of RNA modifications in their native RNA context.

Type Journal
ISBN 2041-1723 (Electronic) 2041-1723 (Linking)
Authors Liu, H.; Begik, O.; Lucas, M. C.; Ramirez, J. M.; Mason, C. E.; Wiener, D.; Schwartz, S.; Mattick, J. S.; Smith, M. A.; Novoa, E. M.
Responsible Garvan Author Dr Eva Maria Novoa Pardo
Publisher Name Nature Communications
Published Date 2019-09-09
Published Volume 10
Published Issue 1
Published Pages 4079
Status Published in-print
DOI 10.1038/s41467-019-11713-9
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/31501426