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RNA Editing pp 163-176 | Cite as

RNA Editing in Human and Mouse Tissues

  • Harini Srinivasan
  • Eng Piew Louis Kok
  • Meng How TanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2181)

Abstract

Adenosine-to-inosine (A-to-I) RNA editing is a fundamental posttranscriptional mechanism that greatly diversifies the transcriptome in many living organisms, including mammals. Multiple studies have demonstrated the importance of this process not just in normal development and physiology but also in various human diseases. Importantly, the precise editing level of a site may have downstream consequences on cellular behavior. Hence, the editing levels should be quantified as accurately as possible. In this chapter, we describe how to examine RNA editing in human and mouse tissues. The rapid development of next-generation sequencing technologies is affording us an unprecedented ability to accurately measure the editing levels of numerous sites simultaneously. Our experimental workflow includes the harvesting of high-quality RNA samples and the construction of different high-throughput sequencing libraries. We also delineate the computational steps needed to analyze the sequencing data from an Illumina platform.

Key words

ADAR RNA editing Epitranscriptome RNA-seq Amplicon sequencing 

References

  1. 1.
    Nishikura K (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321–349.  https://doi.org/10.1146/annurev-biochem-060208-105251CrossRefPubMedPubMedCentralGoogle Scholar
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    Ramaswami G, Li JB (2014) RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res 42(Database issue):D109–D113.  https://doi.org/10.1093/nar/gkt996CrossRefPubMedGoogle Scholar
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    Picardi E, D’Erchia AM, Lo Giudice C, Pesole G (2017) REDIportal: a comprehensive database of A-to-I RNA editing events in humans. Nucleic Acids Res 45(D1):D750–D757.  https://doi.org/10.1093/nar/gkw767CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2021

Authors and Affiliations

  • Harini Srinivasan
    • 1
    • 2
  • Eng Piew Louis Kok
    • 2
  • Meng How Tan
    • 1
    • 2
    Email author
  1. 1.School of Chemical and Biomedical EngineeringNanyang Technological UniversitySingaporeSingapore
  2. 2.Genome Institute of Singapore, Agency for Science Technology and ResearchSingaporeSingapore

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