Nuclear Bodies and Noncoding Rnas: Methods and Protocols

ISBN-13: 9781493922529 / Angielski / Twarda / 2015 / 351 str.

Shinichi Nakagawa; Tetsuro Hirose

Opis

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.

Spis treści

Part I: Imaging of Noncoding RNAs and Nuclear Bodies

1. Visualization of lncRNA by Single Molecule Fluorescence in situ Hybridization

      Margaret Dunagin, Moran N. Cabili, John Rinn, and Arjun Raj

2.      Super-resolution Imaging of Nuclear Bodies by STED Microscopy

Yasushi Okada and Shinichi Nakagawa

3.      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, and Edith Heard

4.      Time-lapse Imaging of Nuclear Bodies

      Saskia Hutten, Samuel Swift, and Angus I. Lamond

5.      Visualization of Nucleic Acids with Synthetic Exciton-controlled Fluorescent Oligonucleotide Probes

Dan Ohtan Wang and Akimitsu Okamoto

6.      Live CLEM Imaging to Analyze Nuclear Structures at High-resolution

Tokuko Haraguchi, Hiroko Osakada, and Takako Koujin

7.      Ultrastructural Analysis of Nuclear Bodies Using Electron Microscopy

Sylvie Souquere and Gérard Pierron

8.      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, Masahiro Kumeta, Shige H. Yoshimura, and Kunio Takeyasu

9.      Genome-wide Co-localization Screening of Nuclear Body Components Using a Fluorescently Tagged FLJ cDNA Clone Library

Tetsuro Hirose and Naoki Goshima

 

Part II: Biochemical Analysis of Noncoding RNAs and Nuclear Bodies

10.  Purification of Specific Chromatin Regions Using Oligonucleotides: Capture Hybridization Analysis of RNA Targets (CHART)

Christopher P. Davis and Jason A. West

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

Jesse Engreitz, Eric S. Lander, and Mitchell Guttman

12.  In situ Dissection of RNA Functional Subunits by Domain-specific Chromatin Isolation by RNA Purification (dChIRP)

Jeffrey J. Quinn and Howard Y. Chang

13.  Extracting, Enriching and Identifying Nuclear Body Sub-complexes Using Label-based Quantitative Mass Spectrometry

Archa Fox, Virja Mehta, Severine Boulon, and Laura Trinkle-Mulcahy

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

Joseph A. Cozzitorto, Maya Jimbo, Saswati Chand, Fernando Blanco, Shruti Lal, Melissa Gilbert, Jordan M. Winter, Myriam Gorospe, and Jonathan R. Brody

15.  Cross-linking and Immunoprecipitation of Nuclear RNA Binding Proteins

      Quan Li, Yuri Uemura, and Yukio Kawahara

16.  Purifications of Non-coding RNA and Bound Proteins using FLAG Peptide-conjugated Antisense-oligonucleotides

Shungo Adachi and Tohru Natsume

         

Part III: Cell and Molecular Biological Approach Towards the Analysis of Noncoding RNAs and Nuclear Bodies

17.  MMCT-Mediated Chromosome Engineering Technique Applicable to Functional Analysis of lncRNA and Nuclear Dynamics

Makiko Meguro-Horike and Shin-ichi Horike

18.  Reconstitution of Nucleocytoplasmic Transport Using Digitonin-Permeabilized Cells

Shingo Kose, Tomoko Funakoshi, and Naoko Imamoto

19.  Genome-wide Analysis of Long Noncoding RNA Turnover

Hidenori Tani, Naoto Imamachi, Rena Mizutani, Katsutoshi Imamura, Yeondae Kwon, Satoru Miyazaki, Sho Maekawa, Yutaka Suzuki, and Nobuyoshi Akimitsu

20.  Knockdown of Nuclear-retained Long Noncoding RNAs Using Modified DNA Antisense Oligonucleotides

Xinying Zong, Lulu Huang, Vidisha Tripathi, Raechel Peralta, Susan M. Freier, Shuling Guo, and Kannanganattu V. Prasanth

21.  siRNA Screening of Nuclear Proteins

Yuko Hasegawa and Shinichi Nakagawa