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piRNA

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Nicholas F. Parrish

    1. Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan

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    You can also search for this editor in PubMed   Google Scholar

  2. Yuka W. Iwasaki

    1. Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2509)

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xii
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  2. Methods to Study the Nature and Function of piRNAs in Non-classical Organisms

    1. Front Matter

      Pages 1-1
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    2. Functional Analysis of Individual piRNAs in Aedes aegypti Cells and Embryos Using Antisense Oligonucleotides

      • Rebecca Halbach, Pascal Miesen
      Pages 3-22

    3. CRISPR-Mediated Genome Engineering in Aedes aegypti

      • Ruichen Sun, Ming Li, Conor J. McMeniman, Omar S. Akbari
      Pages 23-51

    4. PIWI-Directed DNA Elimination for Tetrahymena Genetics

      • Salman Shehzada, Kazufumi Mochizuki
      Pages 53-68

    5. Planarian PIWI–piRNA Interaction Analysis Using Immunoprecipitation and piRNA Sequencing

      • Makoto Kashima, Atsumi Miyata, Norito Shibata
      Pages 69-81

    6. Isolation and Processing of Bovine Oocytes for Small RNA Sequencing

      • Minjie Tan, Helena T. A. van Tol, Elke F. Roovers
      Pages 83-91

    7. 3D Imaging and In Situ Hybridization for Uncovering the Functions of MicroRNA in Rice Anther

      • Koji Koizumi, Reina Komiya
      Pages 93-104

  3. Methods to Study Roles of piRNAs in Classic Model Organisms

    1. Front Matter

      Pages 105-105
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    2. Cloning, Sequencing, and Linkage Analysis of piRNAs

      • Rippei Hayashi
      Pages 107-133

    3. Drosophila Genetic Resources for Elucidating piRNA Pathway

      • Kuniaki Saito
      Pages 135-141

    4. Generation of Stable Drosophila Ovarian Somatic Cell Lines Using the piggyBac System

      • Chikara Takeuchi, Kensaku Murano, Mitsuru Ishikawa, Hideyuki Okano, Yuka W. Iwasaki
      Pages 143-153

  4. Methods to Study Nuclear Regulation by Other Non-coding RNAs

    1. Front Matter

      Pages 155-155
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    2. Whole-Mount RNA FISH Combined with Immunofluorescence for the Analysis of the Telomeric Ribonucleoproteins in the Drosophila Germline

      • Valeriya Morgunova, Maria M. Sukhova, Alla Kalmykova
      Pages 157-169

    3. CRISPR-Mediated Activation of Transposable Elements in Embryonic Stem Cells

      • Akihiko Sakashita, Masaru Ariura, Satoshi H. Namekawa
      Pages 171-194

    4. Method for Evaluating Effects of Non-coding RNAs on Nucleosome Stability

      • Mariko Dacher, Risa Fujita, Tomoya Kujirai, Hitoshi Kurumizaka
      Pages 195-208

    5. Revisiting the Glass Treatment for Single-Molecule Analysis of ncRNA Function

      • Shuting Shen, Masahiro Naganuma, Yukihide Tomari, Hisashi Tadakuma
      Pages 209-231

    6. Low Input Genome-Wide DNA Methylation Analysis with Minimal Library Amplification

      • Wan Kin Au Yeung, Hiroyuki Sasaki
      Pages 233-250

    7. Solid-Support Directional (SSD) RNA-Seq as a Companion Method to CLIP-Seq

      • Abd-El Monsif Shawky, Mahmoud Dondeti, Zissimos Mourelatos, Anastasios Vourekas
      Pages 251-268

    8. UPA-Seq-Based Search Method for Functional lncRNA Candidates

      • Saori Yokoi, Shinichi Nakagawa
      Pages 269-278
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Keywords

About this book

This detailed volume explores newly-developed methods in PIWI-interacting RNAs (piRNAs) research, methods currently applied to other ncRNAs involved in nuclear regulation which can be used to study piRNAs, and piRNA methods applied in non-classical organisms. It also includes several bioinformatic and biophysical methods related to piRNA studies, consistent with the increasing importance of high-throughput sequencing and computational methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and up-to-date, piRNA: Methods and Protocols serves as an ideal guide for researchers seeking to elucidate the numerous mysteries of this area of multicellular biology.

Editors and Affiliations

  • Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan

    Nicholas F. Parrish

  • Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan

    Yuka W. Iwasaki

Bibliographic Information

  • Book Title: piRNA

  • Book Subtitle: Methods and Protocols

  • Editors: Nicholas F. Parrish, Yuka W. Iwasaki

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2380-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2379-4Published: 08 July 2022

  • Softcover ISBN: 978-1-0716-2382-4Published: 08 July 2023

  • eBook ISBN: 978-1-0716-2380-0Published: 07 July 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 397

  • Number of Illustrations: 10 b/w illustrations, 73 illustrations in colour

  • Topics: Chemistry/Food Science, general, Biomaterials, Protein Science

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