PIWI-interacting RNAs
Subtitle: methods and protocols
By: edited by Mikiko C. Siomi, Graduate School of Science, The University of Tokyo, Tokyo, Japan
Series: Methods in molecular biology -- 1093; Springer protocols; Methods in molecular biology (Clifton, N.J.) -- v. 1093.; Springer protocols (Series)
Publisher: Humana Press
Published: 2014
Place of publication: New York
Language: eng
Number of pages: 249
ISBN-13: 9781627036931; 9781627036948
Copyright date: 2014
Subjects: Small interfering RNA; Laboratory manuals; Piwi genes; Small Interfering RNA; Laboratory Manuals; Animal Models
Description: "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."--Publisher's description.
Notes: Includes bibliographical references and index.
Table of contents: title: Chromatin Immunoprecipitation Assay of Piwi in Drosophila  -- Hang Yin and Haifan Lin; title: Drosophila Germline Stem Cells for In Vitro Analyses of PIWI-Mediated RNAi  -- Yuzo Niki, Takuya Sato, Takafumi Yamaguchi, Ayaka Saisho, Hiroshi Uetake, and Hidenori Watanabe; title: RNAi and Overexpression of Genes in Ovarian Somatic Cells  -- Kuniaki Saito; title: Making piRNAs In Vitro  -- Shinpei Kawaoka, Susumu Katsuma, and Yukihide Tomari; title: A Framework for piRNA Cluster Manipulation  -- Ivan Olovnikov, Adrien Le Thomas, and Alexei A. Aravin; title: Biochemical and Mass Spectrometric Analysis of 3ʹ-End Methylation of piRNAs  -- Takeo Suzuki, Kenjyo Miyauchi, Yuriko Sakaguchi, and Tsutomu Suzuki; title: HITS-CLIP (CLIP-Seq) for Mouse Piwi Proteins  -- Anastassios Vourekas and Zissimos Mourelatos; title: DNA Methylation in Mouse Testes  -- Satomi Kuramochi-Miyagawa, Kanako Kita-Kojima, Yusuke Shiromoto, Daisuke Ito, Hirotaka Koshima, and Toru Nakano; title: Analysis of Small RNA-Guided Endonuclease Activity in Endogenous Piwi Protein Complexes from Mouse Testes  -- Michael Reuter and Ramesh S. Pillai; title: Small RNA Library Construction from Minute Biological Samples  -- Jessica A. Matts, Yuliya Sytnikova, Gung-wei Chirn, Gabor L. Igloi, and Nelson C. Lau; title: Analysis of sDMA Modifications of PIWI Proteins  -- Shozo Honda, Yoriko Kirino, and Yohei Kirino; title: Analyses of piRNA-Mediated Transcriptional Transposon Silencing in Drosophila: Nuclear Run-On Assay on Ovaries  -- Sergey Shpiz and Alla Kalmykova; title: Combined RNA/DNA Fluorescence In Situ Hybridization on Whole-Mount Drosophila Ovaries  -- Shpiz, Sergey Lavrov, and Alla Kalmykova; title: Fast and Accurate Method to Purify Small Noncoding RNAs from Drosophila Ovaries  -- Thomas Grentzinger and Séverine Chambeyron; title: Isolation of Zebrafish Gonads for RNA Isolation  -- Hsin-Yi Huang and René F. Ketting; title: Small RNA Library Construction for High-Throughput Sequencing  -- Jon McGinn and Benjamin Czech; title: Analysis of Piwi-Loaded Small RNAs in Terahymena  -- Tomoko Noto, Henriette M. Kurth, and Kazufumi Mochizuki; title: Effective Gene Knockdown in the Drosophila Germline by Artificial miRNA-Mimicking siRNAs  -- Hailong Wang, Haidong Huang, and Dahua Chen; title: Isolation and Bioinformatic Analyses of Small RNAs Interacting with Germ Cell-Specific Argonaute in Rice -- Reina Komiya and Ken-Ichi Nonomura.