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

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

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
JournalMethods
DOIs
Publication statusAccepted/In press - 2017 Mar 28

Fingerprint

High-Throughput Nucleotide Sequencing
Throughput
RNA
Testis
Regulator Genes
Bioinformatics
Multigene Family
Computational Biology
Transcriptome
Gene expression
Small Interfering RNA
Genes

Keywords

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

ASJC Scopus subject areas

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

Cite this

Deep sequencing and high-throughput analysis of PIWI-associated small RNAs. / Iwasaki, Yuka; Ishino, Kyoko; Siomi, Haruhiko.

In: Methods, 28.03.2017.

Research output: Contribution to journalArticle

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