New Twists in Detecting mRNA Modification Dynamics

Ina Anreiter; Quoseena Mir; Jared T Simpson; Sarath C Janga; Matthias Soller

doi:10.1016/j.tibtech.2020.06.002

New Twists in Detecting mRNA Modification Dynamics

Trends Biotechnol. 2021 Jan;39(1):72-89. doi: 10.1016/j.tibtech.2020.06.002. Epub 2020 Jul 1.

Authors

Ina Anreiter¹, Quoseena Mir², Jared T Simpson¹, Sarath C Janga³, Matthias Soller⁴

Affiliations

¹ Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada.
² Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.
³ Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, 5021 Health Information and Translational Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
⁴ School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. Electronic address: m.soller@bham.ac.uk.

Abstract

Modified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucleotide modifications in mRNA and their impact on gene expression. The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions. Selective chemical and immunological identification of modified nucleotides has revealed global candidate topology maps for many modifications in mRNA, but further technical advances to increase confidence will be necessary. Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel sequencing technology.

Keywords: 2′-O-ribose methylation; Nanopore; m(5)C; m(6)A; m(6)Am; mRNA modifications.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Animals
Computational Biology* / trends
Mutation / genetics
RNA, Messenger* / genetics
Sequence Analysis, RNA / trends

Substances

RNA, Messenger

Grants and funding

R01 GM123314/GM/NIGMS NIH HHS/United States