Nuclear bodies and noncoding RNAs
Subtitle: methods and protocols
By: edited by Shinichi Nakagawa, RNA Biology Laboratory, REIKEN, Saitama, Japan, Tetsuro Hirose, Institute for Genetic Medicine, Hokkaido University, Sappora, Japan
Contributors: Springer Science+Business Media
Series: Methods in molecular biology -- 1262; Springer protocols; Methods in molecular biology -- v. 1262.; Springer protocols (Series)
Publisher: Humana Press
Published: 2015
Place of publication: New York
Language: eng
Number of pages: 351
ISBN-13: 9781493922529; 9781493922536
Copyright date: 2015
Subjects: Cell Nucleus; Genetics; Non-coding RNA; Laboratory Manuals; Untranslated RNA; Nuclear proteins; Laboratory manuals; Metabolism; Nuclear Proteins
Description: 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.
Notes: Includes bibliographical references and index.
Table of contents: title: Visualization of lncRNA by single-molecule fluorescence in situ hybridization  -- Margaret Dunagin , Moran N. Cabili , John Rinn , and Arjun Raj; title: Super-resolution imaging of nuclear bodies by STED microscopy  -- Yasushi Okada and Shinichi Nakagawa; title: 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; title: Time-lapse imaging of nuclear bodies  -- Saskia Hutten, Samuel Swift, and Angus I. Lamond; title: Visualization of nucleic acids with synthetic exciton-controlled fluorescent oligonucleotide probes  -- Dan Ohtan Wang and Akimitsu Okamoto; title: Live CLEM imaging to analyze nuclear structures at high resolution  -- Tokuko Haraguchi, Hiroko Osakada, and Takako Koujin; title: Ultrastructural analysis of nuclear bodies using electron microscopy  -- Sylvie Souquere and Gérard Pierron; title: Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy  -- Jamie L. Gilmore [and eight others]; title: Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library  -- Tetsuro Hirose and Naoki Goshima; title: Purification of specific chromatin regions using oligonucleotides : capture hybridization analysis of RNA targets (CHART)  -- Christopher P. Davis and Jason A. West; title: RNA antisense purification (RAP) for mapping RNA interactions with chromatin  -- Jesse Engreitz, Eric S. Lander, and Mitchell Guttman; title: In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP)  -- Jeffrey J. Quinn and Howard Y. Chang; title: Extracting, enriching, and identifying nuclear body sub-complexes using label-based quantitative mass spectrometry  -- Archa Fox [and three othrs]; title: Studying RNA-binding protein interactions with target mRNAs in eukaryotic cells : native ribonucleoprotein immunoprecipitation (RIP) assays  -- Joseph A. Cozzitorto [and eight others]; title: Cross-linking and immunoprecipitation of nuclear RNA-binding proteins  -- Quan Li , Yuri Uemura , and Yukio Kawahara; title: Purification of noncoding RNA and bound proteins using FLAG peptide-conjugated antisense-oligonucleotides  -- Shungo Adachi and Tohru Natsume; title: MMCT-mediated chromosome engineering technique applicable to functional analysis of lncRNA and nuclear dynamics  -- Makiko Meguro-Horike and Shin-ichi Horike; title: Reconstitution of nucleocytoplasmic transport using digitonin-permeabilized cells  -- Shingo Kose, Tomoko Funakoshi, and Naoko Imamoto; title: Genome-wide analysis of long noncoding RNA turnover  -- Hidenori Tani [and eight others]; title: Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides  -- Xinying Zong [and  six others]; title: siRNA screening of nuclear proteins -- Yuko Hasegawa and Shinichi Nakagawa.