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Nuclear Bodies and Noncoding RNAs

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Shinichi Nakagawa

    1. RNA Biology Laboratory, RIKEN, Saitama, Japan

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Tetsuro Hirose

    1. Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • 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 1262)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Imaging of Noncoding RNAs and Nuclear Bodies

    1. Front Matter

      Pages 1-1
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    2. Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

      • Margaret Dunagin, Moran N. Cabili, John Rinn, Arjun Raj
      Pages 3-19

    3. Super-Resolution Imaging of Nuclear Bodies by STED Microscopy

      • Yasushi Okada, Shinichi Nakagawa
      Pages 21-35

    4. High-Resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale

      • Luca Giorgetti, Tristan Piolot, Edith Heard
      Pages 37-53

    5. Time-Lapse Imaging of Nuclear Bodies

      • Saskia Hutten, Samuel Swift, Angus I. Lamond
      Pages 55-67

    6. Visualization of Nucleic Acids with Synthetic Exciton-Controlled Fluorescent Oligonucleotide Probes

      • Dan Ohtan Wang, Akimitsu Okamoto
      Pages 69-87

    7. Live CLEM Imaging to Analyze Nuclear Structures at High Resolution

      • Tokuko Haraguchi, Hiroko Osakada, Takako Koujin
      Pages 89-103

    8. Ultrastructural Analysis of Nuclear Bodies Using Electron Microscopy

      • Sylvie Souquere, Gérard Pierron
      Pages 105-118

    9. Analyses of Nuclear Proteins and Nucleic Acid Structures Using Atomic Force Microscopy

      • Jamie L. Gilmore, Aiko Yoshida, Hirohide Takahashi, Katashi Deguchi, Toshiro Kobori, Emilie Louvet et al.
      Pages 119-153

    10. Genome-Wide Co-Localization Screening of Nuclear Body Components Using a Fluorescently Tagged FLJ cDNA Clone Library

      • Tetsuro Hirose, Naoki Goshima
      Pages 155-163

  3. Biochemical Analysis of Noncoding RNAs and Nuclear Bodies

    1. Front Matter

      Pages 165-165
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    2. Purification of Specific Chromatin Regions Using Oligonucleotides: Capture Hybridization Analysis of RNA Targets (CHART)

      • Christopher P. Davis, Jason A. West
      Pages 167-182

    3. RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin

      • Jesse Engreitz, Eric S. Lander, Mitchell Guttman
      Pages 183-197

    4. In Situ Dissection of RNA Functional Subunits by Domain-Specific Chromatin Isolation by RNA Purification (dChIRP)

      • Jeffrey J. Quinn, Howard Y. Chang
      Pages 199-213

    5. Extracting, Enriching, and Identifying Nuclear Body Sub-Complexes Using Label-Based Quantitative Mass Spectrometry

      • Archa Fox, Virja Mehta, Severine Boulon, Laura Trinkle-Mulcahy
      Pages 215-238

    6. Studying RNA-Binding Protein Interactions with Target mRNAs in Eukaryotic Cells: Native Ribonucleoprotein Immunoprecipitation (RIP) Assays

      • Joseph A. Cozzitorto, Masaya Jimbo, Saswati Chand, Fernando Blanco, Shruti Lal, Melissa Gilbert et al.
      Pages 239-246

    7. Cross-Linking and Immunoprecipitation of Nuclear RNA-Binding Proteins

      • Quan Li, Yuri Uemura, Yukio Kawahara
      Pages 247-263

    8. Purification of Noncoding RNA and Bound Proteins Using FLAG Peptide-Conjugated Antisense-Oligonucleotides

      • Shungo Adachi, Tohru Natsume
      Pages 265-274

  4. Cell and Molecular Biological Approach Toward the Analysis of Noncoding RNAs and Nuclear Bodies

    1. Front Matter

      Pages 275-275
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Keywords

About this book

This volume focuses on cytological, biochemical, and molecular biological methods to identify and examine the function of each nuclear body, with an emphasis on the analysis of long non-coding RNAs. Chapters focus on exploring recent studies that reveal how certain long non protein-coding RNAs accumulate in specific nuclear bodies and regulate the function of the bodies by serving as architectural components or controlling the dynamics of associating protein components. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Nuclear Bodies and Noncoding RNAs: Methods and Protocols serves as a guideline for further study into the sophisticated regulation of gene expression.

Editors and Affiliations

  • RNA Biology Laboratory, RIKEN, Saitama, Japan

    Shinichi Nakagawa

  • Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan

    Tetsuro Hirose

Bibliographic Information

  • Book Title: Nuclear Bodies and Noncoding RNAs

  • Book Subtitle: Methods and Protocols

  • Editors: Shinichi Nakagawa, Tetsuro Hirose

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-2253-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2252-9Published: 02 January 2015

  • Softcover ISBN: 978-1-4939-5549-7Published: 05 October 2016

  • eBook ISBN: 978-1-4939-2253-6Published: 02 January 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 351

  • Number of Illustrations: 24 b/w illustrations, 46 illustrations in colour

  • Topics: Human Genetics, Gene Function

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