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

研究成果: Chapter

5 被引用数 (Scopus)

抄録

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.

本文言語English
ホスト出版物のタイトルMethods in Molecular Biology
出版社Humana Press Inc.
ページ167-183
ページ数17
DOI
出版ステータスPublished - 2018

出版物シリーズ

名前Methods in Molecular Biology
1823
ISSN(印刷版)1064-3745

ASJC Scopus subject areas

  • 分子生物学
  • 遺伝学

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