Nuclear Bodies and Noncoding RNAs : Methods and Protocols - Nakagawa, Shinichi; Hirose, Tetsuro; SpringerLink (Online service) (New York, NY : Springer New York : Imprint: Humana, 2015)
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.
Keywords: Human genetics; Medical genetics; Human Genetics; Gene Function