Nuclear bodies and noncoding RNAs : methods and protocols / edited by Shinichi Nakagawa, Tetsuro Hirose.

Contributor(s): Nakagawa, Shinichi [editor.] | Hirose, Tetsurō [editor.]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 1262.Publisher: New York, NY : Humana Press, [2015]Copyright date: ©2015Description: 1 online resource (xiiI, 351 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781493922536; 149392253X; 1493922521; 9781493922529Subject(s): Non-coding RNA -- Laboratory manuals | Nuclear proteins -- Laboratory manuals | RNA | Organelles | Clinical Laboratory Techniques | Metabolism | Intracellular Space | Proteins | Publication Formats | Biology | Publication Characteristics | Nucleic Acids | Cellular Structures | Cytoplasmic Structures | Biological Science Disciplines | Investigative Techniques | Amino Acids, Peptides, and Proteins | Phenomena and Processes | Chemicals and Drugs | Cells | Natural Science Disciplines | Cytoplasm | Analytical, Diagnostic and Therapeutic Techniques and Equipment | Nucleic Acids, Nucleotides, and Nucleosides | Anatomy | Disciplines and Occupations | Cell Nucleus | Laboratory Manuals | Genetics | Nuclear Proteins | Cell Nucleus Structures | Cytological Techniques | RNA, Untranslated | Medical genetics | Medical -- Genetics | Non-coding RNA | Nuclear proteins | biomedische wetenschappen | biomedicine | moleculaire genetica | molecular genetics | humane genetica | human genetics | Medicine (General) | Geneeskunde (algemeen)Genre/Form: Electronic books. | Laboratory manuals. Additional physical formats: Print version:: Nuclear bodies and noncoding RNAs.DDC classification: 572.8/8 LOC classification: QP623Online resources: Click here to access online
Contents:
Visualization of lncRNA by single-molecule fluorescence in situ hybridization / Margaret Dunagin, Moran N. Cabili, John Rinn, and Arjun Raj -- Super-resolution imaging of nuclear bodies by STED microscopy / Yasushi Okada and Shinichi Nakagawa -- 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 -- Time-lapse imaging of nuclear bodies / Saskia Hutten, Samuel Swift, and Angus I. Lamond -- Visualization of nucleic acids with synthetic exciton- controlled fluorescent oligonucleotide probes / Dan Ohtan Wang and Akimitsu Okamoto -- Live CLEM imaging to analyze nuclear structures at high resolution / Tokuko Haraguchi, Hiroko Osakada, and Takako Koujin -- Ultrastructural analysis of nuclear bodies using electron microscopy / Sylvie Souquere and Gérard Pierron -- Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy / Jamie L. Gilmore [and others] -- Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library / Tetsuro Hirose and Naoki Goshima -- Purification of specific chromatin regions using oligonucleotides : capture hybridization analysis of RNA targets (CHART) / Christopher P. Davis and Jason A. West -- RNA antisense purification (RAP) for mapping RNA interactions with chromatin / Jesse Engreitz, Eric S. Lander, and Mitchell Guttman -- In situ dissection of RNA functional subunits by domain- specific chromatin isolation by RNA purification (dChIRP) / Jeffrey J. Quinn and Howard Y. Chang -- Extracting, enriching, and identifying nuclear body sub-complexes using label-based quantitative mass spectrometry / Archa Fox [and others] -- Studying RNA-binding protein interactions with target mRNAs in eukaryotic cells : native ribonucleoprotein immunoprecipitation (RIP) assays / Joseph A. Cozzitorto [and others] -- Cross-linking and immunoprecipitation of nuclear RNA- binding proteins / Quan Li, Yuri Uemura, and Yukio Kawahara -- Purification of noncoding RNA and bound proteins using FLAG peptide-conjugated antisense-oligonucleotides / Shungo Adachi and Tohru Natsume -- MMCT-mediated chromosome engineering technique applicable to functional analysis of lncRNA and nuclear dynamics / Makiko Meguro-Horike and Shin-ichi Horike -- Reconstitution of nucleocytoplasmic transport using digitonin-permeabilized cells / Shingo Kose, Tomoko Funakoshi, and Naoko Imamoto -- Genome-wide analysis of long noncoding RNA turnover / Hidenori Tani [and others] -- Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides / Xinying Zong [and others] -- siRNA screening of nuclear proteins / Yuko Hasegawa and Shinichi Nakagawa.
Summary: 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.
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Includes bibliographical references and index.

Visualization of lncRNA by single-molecule fluorescence in situ hybridization / Margaret Dunagin, Moran N. Cabili, John Rinn, and Arjun Raj -- Super-resolution imaging of nuclear bodies by STED microscopy / Yasushi Okada and Shinichi Nakagawa -- 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 -- Time-lapse imaging of nuclear bodies / Saskia Hutten, Samuel Swift, and Angus I. Lamond -- Visualization of nucleic acids with synthetic exciton- controlled fluorescent oligonucleotide probes / Dan Ohtan Wang and Akimitsu Okamoto -- Live CLEM imaging to analyze nuclear structures at high resolution / Tokuko Haraguchi, Hiroko Osakada, and Takako Koujin -- Ultrastructural analysis of nuclear bodies using electron microscopy / Sylvie Souquere and Gérard Pierron -- Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy / Jamie L. Gilmore [and others] -- Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library / Tetsuro Hirose and Naoki Goshima -- Purification of specific chromatin regions using oligonucleotides : capture hybridization analysis of RNA targets (CHART) / Christopher P. Davis and Jason A. West -- RNA antisense purification (RAP) for mapping RNA interactions with chromatin / Jesse Engreitz, Eric S. Lander, and Mitchell Guttman -- In situ dissection of RNA functional subunits by domain- specific chromatin isolation by RNA purification (dChIRP) / Jeffrey J. Quinn and Howard Y. Chang -- Extracting, enriching, and identifying nuclear body sub-complexes using label-based quantitative mass spectrometry / Archa Fox [and others] -- Studying RNA-binding protein interactions with target mRNAs in eukaryotic cells : native ribonucleoprotein immunoprecipitation (RIP) assays / Joseph A. Cozzitorto [and others] -- Cross-linking and immunoprecipitation of nuclear RNA- binding proteins / Quan Li, Yuri Uemura, and Yukio Kawahara -- Purification of noncoding RNA and bound proteins using FLAG peptide-conjugated antisense-oligonucleotides / Shungo Adachi and Tohru Natsume -- MMCT-mediated chromosome engineering technique applicable to functional analysis of lncRNA and nuclear dynamics / Makiko Meguro-Horike and Shin-ichi Horike -- Reconstitution of nucleocytoplasmic transport using digitonin-permeabilized cells / Shingo Kose, Tomoko Funakoshi, and Naoko Imamoto -- Genome-wide analysis of long noncoding RNA turnover / Hidenori Tani [and others] -- Knockdown of nuclear-retained long noncoding RNAs using modified DNA antisense oligonucleotides / Xinying Zong [and others] -- siRNA screening of nuclear proteins / Yuko Hasegawa and Shinichi Nakagawa.

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.

Online resource; title from PDF title page (SpringerLink, viewed January 23, 2015).

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