High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA

Josephine Galipon, Rintaro Ishii, Soh Ishiguro, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei

Research output: Chapter in Book/Report/Conference proceeding › Chapter

1 Citation (Scopus)

Abstract

Paired-end RNA sequencing (RNA-seq) is usually applied to the quantification of long transcripts such as messenger or long non-coding RNAs, in which case overlapping pairs are discarded. In contrast, RNA-seq on short RNAs (≤ 200 nt) is typically carried out in single-end mode, as the additional cost associated with paired-end would only translate into redundant sequence information. Here, we exploit paired-end sequencing of short RNAs as a strategy to filter out sequencing errors and apply this method to the identification of adenosine-to-inosine (A-to-I) RNA editing events on human precursor microRNA (pre-miRNA) and mature miRNA. Combined with RNA immunoprecipitation sequencing (RIP-seq) of A-to-I RNA editing enzymes, this method takes full advantage of deep sequencing technology to identify RNA editing sites with unprecedented resolution in terms of editing efficiency.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages167-183
Number of pages17
DOIs
Publication statusPublished - 2018 Jan 1

Publication series

NameMethods in Molecular Biology
Volume1823
ISSN (Print)1064-3745

Fingerprint

RNA Sequence Analysis
Inosine
RNA Editing
Adenosine
RNA
MicroRNAs
Long Noncoding RNA
High-Throughput Nucleotide Sequencing
Immunoprecipitation
Technology
Costs and Cost Analysis
Enzymes

Keywords

  • Inosine
  • microRNA
  • Paired-end sequencing
  • RNA editing
  • RNA-seq
  • Small RNA

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Galipon, J., Ishii, R., Ishiguro, S., Suzuki, Y., Kondo, S., Okada-Hatakeyama, M., ... Ui-Tei, K. (2018). High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA. In Methods in Molecular Biology (pp. 167-183). (Methods in Molecular Biology; Vol. 1823). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-8624-8_13

High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA. / Galipon, Josephine; Ishii, Rintaro; Ishiguro, Soh; Suzuki, Yutaka; Kondo, Shinji; Okada-Hatakeyama, Mariko; Tomita, Masaru; Ui-Tei, Kumiko.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 167-183 (Methods in Molecular Biology; Vol. 1823).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Galipon, J, Ishii, R, Ishiguro, S, Suzuki, Y, Kondo, S, Okada-Hatakeyama, M, Tomita, M & Ui-Tei, K 2018, High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1823, Humana Press Inc., pp. 167-183. https://doi.org/10.1007/978-1-4939-8624-8_13
Galipon J, Ishii R, Ishiguro S, Suzuki Y, Kondo S, Okada-Hatakeyama M et al. High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA. In Methods in Molecular Biology. Humana Press Inc. 2018. p. 167-183. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-8624-8_13
Galipon, Josephine ; Ishii, Rintaro ; Ishiguro, Soh ; Suzuki, Yutaka ; Kondo, Shinji ; Okada-Hatakeyama, Mariko ; Tomita, Masaru ; Ui-Tei, Kumiko. / High-quality overlapping paired-end reads for the detection of A-to-I editing on small RNA. Methods in Molecular Biology. Humana Press Inc., 2018. pp. 167-183 (Methods in Molecular Biology).
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