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RNA Editing pp 113-148 | Cite as

Discovering A-to-I RNA Editing Through Chemical Methodology “ICE-seq”

  • Masayuki SakuraiEmail author
  • Shunpei Okada
  • Hiroki Ueda
  • Yuxi Yang
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2181)

Abstract

手机体育投注平台RNA editing of adenosines to inosines contributes to a wide range of biological processes by regulating gene expression post-transcriptionally. To understand the effect, accurate mapping of inosines is necessary. The most conventional method to identify an editing site is to compare the cDNA sequence with its corresponding genomic sequence. However, this method has a high false discovery rate because guanosine signals, due to experimental errors or noise in the obtained sequences, contaminate genuine inosine signals detected as guanosine. To ensure high accuracy, we developed the Inosine Chemical Erasing (ICE) method to accurately and biochemically identify inosines in RNA strands utilizing inosine cyanoethylation and reverse transcription-PCR. Furthermore, we applied this technique to next-generation sequencing technology, called ICE-seq, to conduct an unbiased genome-wide screening of A-to-I editing sites in the transcriptome.

Key words

A-to-I RNA editing Inosine cyanoethylation ICE-seq 

Notes

Acknowledgments

We express our deepest gratitude to Dr. Suzuki at the University of Tokyo for his supervision and contribution to the original development of ICE-seq at his laboratory. We are grateful to Drs. Atsushi Toyoda (NIG), Asao Fujiyama (NIG), and Toutai Mitsuyama (AIST) for their support in performing deep sequencing and computation. This work and updating of the manuscript were supported by Grants-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports, and Culture of Japan (MEXT) and the Japan Society for the Promotion of Science (JSPS) (to M.S., S.O., and Dr. Suzuki).

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Copyright information

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

Authors and Affiliations

  • Masayuki Sakurai
    • 1
    Email author
  • Shunpei Okada
    • 1
  • Hiroki Ueda
    • 2
  • Yuxi Yang
    • 1
  1. 1.Research Institute for Biomedical SciencesTokyo University of ScienceChibaJapan
  2. 2.Biological Data Science Division, Research Center for Advanced Science and Technology (RCAST)University of TokyoTokyoJapan

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