MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq

Mitchell G Kluesner; Rafail Nikolaos Tasakis; Taga Lerner; Annette Arnold; Sandra Wüst; Marco Binder; Beau R Webber; Branden S Moriarity; Riccardo Pecori

doi:10.1016/j.omtn.2021.07.008

MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq

Mol Ther Nucleic Acids. 2021 Jul 21:25:515-523. doi: 10.1016/j.omtn.2021.07.008. eCollection 2021 Sep 3.

Authors

Mitchell G Kluesner^{1

2

3

4

5

6}, Rafail Nikolaos Tasakis^{7

8}, Taga Lerner^{7

8}, Annette Arnold⁷, Sandra Wüst⁹, Marco Binder⁹, Beau R Webber^{1

2

3

4}, Branden S Moriarity^{1

2

3

4}, Riccardo Pecori⁷

Affiliations

¹ Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA.
² Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
³ Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
⁴ Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA.
⁵ University of Washington School of Medicine, Seattle, WA 98195, USA.
⁶ Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA.
⁷ Division of Immune Diversity, Program in Cancer Immunology, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany.
⁸ Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.
⁹ Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response," Division Virus Associated Carcinogenesis (F170), German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany.

Abstract

We present MultiEditR (Multiple Edit Deconvolution by Inference of Traces in R), the first algorithm specifically designed to detect and quantify RNA editing from Sanger sequencing (z.umn.edu/multieditr). Although RNA editing is routinely evaluated by measuring the heights of peaks from Sanger sequencing traces, the accuracy and precision of this approach has yet to be evaluated against gold standard next-generation sequencing methods. Through a comprehensive comparison to RNA sequencing (RNA-seq) and amplicon-based deep sequencing, we show that MultiEditR is accurate, precise, and reliable for detecting endogenous and programmable RNA editing.

Keywords: ADAR; APOBEC; DNA base editing; Epitranscriptomics; MultiEditR Editing Index; RNA editing detection; RNA editing quantification; RNA modification; RShiny; deaminases.