Deep sequencing and high-throughput analysis of PIWI-associated small RNAs

Yuka W. Iwasaki, Kyoko Ishino, Haruhiko Siomi

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)


Small RNAs are now known to be major regulatory factors of gene expression. Emerging methods based on deep-sequencing have enabled the analysis of small RNA expression in a high-throughput manner, leading to the identification of large numbers of small RNAs in various species. Moreover, profiling small RNA data together with transcriptome data enables transcriptional and post-transcriptional regulation mediated by small RNAs to be hypothesized. Here, we isolated PIWIL1 (MIWI)-associated small RNAs from mouse testes, and performed small RNA-seq analysis. In addition, directional RNA-seq was performed using Piwil1 mutant mouse testes. Using these data, we describe protocols for analyzing small RNA-seq reads to obtain profiles of small RNAs associated with PIWI proteins. We also present bioinformatic protocols for analyzing RNA-seq reads that aim to annotate expression of piRNA clusters and identify genes regulated by piRNAs.

Original languageEnglish
Pages (from-to)66-75
Number of pages10
Publication statusPublished - 2017 Aug 15


  • Directional RNA-seq
  • PIWI-piRNA
  • RNA silencing
  • Small RNA-seq

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)


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