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PIWI-Interacting RNAs

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Mikiko C. Siomi

    1. The University of Tokyo Dept of Biophysics & Biochemistry, Tokyo, Japan

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1093)

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About this book

PIWI-interacting RNAs (piRNAs) are the third and most-recently discovered group of silencing-inducible small RNAs in animals. PIWI-Interacting RNAs: Methods and Protocols provides the most recent methods and protocols for studying piRNAs in the gonads of a wide range of species, as well as in any other organs where piRNAs may be detected. Comprehensive high-throughput sequencing analysis of piRNAs in embryos, testes and ovaries of D. melanogaster, as well as in mouse and rat testes, has raised the profile of piRNAs and thus further accelerated piRNA studies. In addition to C. elegans, other model species such as Drosophila melanogaster, Arabidopsis thaliana and mice, along with cultured cell lines such as HeLa and Drosophila Schneider 2 (S2), and other such organisms have been used to address the fundamental questions of the biogenesis and functions of RNAi-triggering small non-coding RNAs. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, PIWI-Interacting RNAs: Methods and Protocols seeks to serve both established researchers and newcomers to the field to progress towards the ultimate goal of understanding the mechanisms and actions of piRNAs.

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Keywords

Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Chromatin Immunoprecipitation Assay of Piwi in Drosophila

    • Hang Yin, Haifan Lin
    Pages 1-11

  3. Drosophila Germline Stem Cells for In Vitro Analyses of PIWI-Mediated RNAi

    • Yuzo Niki, Takuya Sato, Takafumi Yamaguchi, Ayaka Saisho, Hiroshi Uetake, Hidenori Watanabe
    Pages 13-23

  4. RNAi and Overexpression of Genes in Ovarian Somatic Cells

    • Kuniaki Saito
    Pages 25-33

  5. Making piRNAs In Vitro

    • Shinpei Kawaoka, Susumu Katsuma, Yukihide Tomari
    Pages 35-46

  6. A Framework for piRNA Cluster Manipulation

    • Ivan Olovnikov, Adrien Le Thomas, Alexei A. Aravin
    Pages 47-58

  7. Biochemical and Mass Spectrometric Analysis of 3’-End Methylation of piRNAs

    • Takeo Suzuki, Kenjyo Miyauchi, Yuriko Sakaguchi, Tsutomu Suzuki
    Pages 59-72

  8. HITS-CLIP (CLIP-Seq) for Mouse Piwi Proteins

    • Anastassios Vourekas, Zissimos Mourelatos
    Pages 73-95

  9. DNA Methylation in Mouse Testes

    • Satomi Kuramochi-Miyagawa, Kanako Kita-Kojima, Yusuke Shiromoto, Daisuke Ito, Hirotaka Koshima, Toru Nakano
    Pages 97-109

  10. Analysis of Small RNA-Guided Endonuclease Activity in Endogenous Piwi Protein Complexes from Mouse Testes

    • Michael Reuter, Ramesh S. Pillai
    Pages 111-121

  11. Small RNA Library Construction from Minute Biological Samples

    • Jessica A. Matts, Yuliya Sytnikova, Gung-wei Chirn, Gabor L. Igloi, Nelson C. Lau
    Pages 123-136

  12. Analysis of sDMA Modifications of PIWI Proteins

    • Shozo Honda, Yoriko Kirino, Yohei Kirino
    Pages 137-148

  13. Analyses of piRNA-Mediated Transcriptional Transposon Silencing in Drosophila: Nuclear Run-On Assay on Ovaries

    • Sergey Shpiz, Alla Kalmykova
    Pages 149-159

  14. Combined RNA/DNA Fluorescence In Situ Hybridization on Whole-Mount Drosophila Ovaries

    • Sergey Shpiz, Sergey Lavrov, Alla Kalmykova
    Pages 161-169

  15. Fast and Accurate Method to Purify Small Noncoding RNAs from Drosophila Ovaries

    • Thomas Grentzinger, Séverine Chambeyron
    Pages 171-182

  16. Isolation of Zebrafish Gonads for RNA Isolation

    • Hsin-Yi Huang, René F. Ketting
    Pages 183-194

  17. Small RNA Library Construction for High-Throughput Sequencing

    • Jon McGinn, Benjamin Czech
    Pages 195-208

  18. Analysis of Piwi-Loaded Small RNAs in Terahymena

    • Tomoko Noto, Henriette M. Kurth, Kazufumi Mochizuki
    Pages 209-224

  19. Effective Gene Knockdown in the Drosophila Germline by Artificial miRNA-Mimicking siRNAs

    • Hailong Wang, Haidong Huang, Dahua Chen
    Pages 225-234

  20. Isolation and Bioinformatic Analyses of Small RNAs Interacting with Germ Cell-Specific Argonaute in Rice

    • Reina Komiya, Ken-Ichi Nonomura
    Pages 235-245
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Editors and Affiliations

  • The University of Tokyo Dept of Biophysics & Biochemistry, Tokyo, Japan

    Mikiko C. Siomi

Bibliographic Information

  • Book Title: PIWI-Interacting RNAs

  • Book Subtitle: Methods and Protocols

  • Editors: Mikiko C. Siomi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-694-8

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2014

  • Hardcover ISBN: 978-1-62703-693-1Published: 01 November 2013

  • Softcover ISBN: 978-1-4939-6298-3Published: 23 August 2016

  • eBook ISBN: 978-1-62703-694-8Published: 31 October 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 249

  • Number of Illustrations: 25 b/w illustrations, 23 illustrations in colour

  • Topics: Human Genetics

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