Tagging and Application of RNA Probes for Sequence-Specific Visualization of RNAs by Fluorescent In Situ Hybridization -- Quantitative Fluorescence In Situ Hybridization Detection of Plant mRNAs with Single-Molecule Resolution -- Visualization of Endoplasmic Reticulum-Associated mRNA in Mammalian Cells -- Simultaneous Detection of mRNA and Protein in S. cerevisiae by Single Molecule FISH and Immunofluorescence -- Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More -- Visualization of Transiently Expressed mRNA in Plants Using MS2 -- New Generations of MS2 Variants and MCP Fusions to Detect Single mRNAs in Living Eukaryotic Cells -- In Vivo Imaging of Mobile mRNAs in Plants Using MS2 -- RNA Imaging with RNase-Inactivated Csy4 in Plants and Filamentous Fungi -- Utilizing Potato Virus X to Monitor RNA Movement -- A Protocol for Non-Biased Identification of RNAs Transferred between Heterologous Mammalian Cell Types Using RNA Tagging, Cell Sorting, and Sequencing -- Synthesizing Fluorescently Labeled dsRNAs and sRNAs to Visualize Fungal RNA Uptake -- Labeling of dsRNA for Fungal Uptake Detection Analysis -- Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs) -- Plant Individual Nucleotide Resolution Crosslinking and Immunoprecipitation to Characterize RNA-Protein Complexes -- A Single-Molecule RNA Mobility Assay to Identify Proteins that Link RNAs to Molecular Motors -- Proximity-CLIP Provides a Snapshot of Protein-Occupied RNA Elements at Subcellular Resolution and Transcriptome-Wide Scale -- Double-Stranded RNA Pull-Down to Characterize Viral Replication Complexes in Plants -- CRISPR Guide RNA Design Guidelines for Efficient Genome Editing -- Live Cell CRISPR Imaging in Plant Cells with a Telomere-Specific Guide RNA -- Live-Cell Imaging of Genomic Loci Using CRISPR/Molecular Beacon Hybrid Systems -- Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos -- Integrated Genome-Scale Analysis and Northern Blot Detection of Retrotransposon siRNAs across Plant Species -- Transfection of Small Non-Coding RNAs into Arabidopsis thaliana Protoplasts -- In Vivo Reporter System for miRNA-Mediated RNA Silencing -- TRAP-SEQ of Eukaryotic Translatomes Applied to the Detection of Polysome-Associated Long Non-Coding RNAs -- Posttranscriptional Suzuki-Miyaura Cross-Coupling Yields Labeled RNA for Conformational Analysis and Imaging.

This book provides a compendium of state-of-the-art methods for the labeling, detection, and purification of RNA and RNA-protein complexes and thereby constitutes an important toolbox for researchers interested in understanding the complex roles of RNA molecules in development, signaling, and disease. Beginning with a section on in situ detection of RNA molecules using FISH techniques, the volume continues with parts exploring in vivo imaging of RNA transport and localization, imaging and analysis of RNA uptake and transport between cells, identification and analysis of RNA-binding proteins, guide RNAs in genome editing, as well as other specific analytical techniques. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Tagging: Methods and Protocols serves as a vital reference for researchers looking to further the increasingly important research in RNA biology.