Visualization of lncRNA by Single Molecule Fluorescence in situ Hybridization -- Super-resolution Imaging of Nuclear Bodies by STED Microscopy -- High-resolution 3D DNA FISH Using Plasmid Probes and Computational Correction of Optical Aberrations to Study Chromatin Structure at the Sub-megabase Scale -- Time-lapse Imaging of Nuclear Bodies -- Visualization of Nucleic Acids with Synthetic Exciton-controlled Fluorescent Oligonucleotide Probes -- Live CLEM Imaging to Analyze Nuclear Structures at High-resolution -- Ultrastructural Analysis of Nuclear Bodies Using Electron Microscopy -- Analyses of Nuclear Proteins and Nucleic Acid Structures Using Atomic Force Microscopy -- Genome-wide Co-localization Screening of Nuclear Body Components Using a Fluorescently Tagged FLJ cDNA Clone Library -- Purification of Specific Chromatin Regions Using Oligonucleotides: Capture Hybridization Analysis of RNA Targets (CHART) -- RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin -- In situ Dissection of RNA Functional Subunits by Domain-specific Chromatin Isolation by RNA Purification (dChIRP) -- Extracting, Enriching and Identifying Nuclear Body Sub-complexes Using Label-based Quantitative Mass Spectrometry -- Studying RNA-binding Protein Interactions with Target mRNAs in Eukaryotic Cells: Native Ribonucleoprotein Immunoprecipitation (RIP) Assays -- Cross-linking and Immunoprecipitation of Nuclear RNA Binding Proteins -- Purifications of Non-coding RNA and Bound Proteins using FLAG Peptide-conjugated Antisense-oligonucleotides -- MMCT-Mediated Chromosome Engineering Technique Applicable to Functional Analysis of lncRNA and Nuclear Dynamics -- Reconstitution of Nucleocytoplasmic Transport Using Digitonin-Permeabilized Cells -- Genome-wide Analysis of Long Noncoding RNA Turnover -- Knockdown of Nuclear-retained Long Noncoding RNAs Using Modified DNA Antisense Oligonucleotides -- siRNA Screening of Nuclear Proteins.

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.