MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq
| Autor: | Marco Binder, Sandra Wüst, Riccardo Pecori, Mitchell G. Kluesner, Taga Lerner, Annette Arnold, Branden S. Moriarity, Beau R. Webber, Rafail Nikolaos Tasakis |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Computer science
RNA-Seq Computational biology RM1-950 Deep sequencing 03 medical and health sciences symbols.namesake RShiny 0302 clinical medicine Epitranscriptomics Drug Discovery deaminases RNA editing quantification natural sciences 030304 developmental biology Sanger sequencing MultiEditR Editing Index 0303 health sciences RNA editing detection APOBEC RNA Amplicon RNA modification ADAR RNA editing symbols Molecular Medicine Original Article Therapeutics. Pharmacology 030217 neurology & neurosurgery DNA base editing |
| Zdroj: | Molecular Therapy: Nucleic Acids, Vol 25, Iss, Pp 515-523 (2021) Molecular Therapy. Nucleic Acids |
| ISSN: | 2162-2531 |
| Popis: | 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. Graphical abstract RNA editing allows cells to transiently rewrite the genetic code. However, detecting and quantifying RNA editing relies on RNA-seq, which is expensive and suffers from poor local resolution. Here, we develop MultiEditR (https://moriaritylab.shinyapps.io/multieditr/) to analyze RNA editing from Sanger sequencing for a fraction of the cost while maintaining a comparable fidelity to RNA-seq. |
| Databáze: | OpenAIRE |
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