RNA Detection and Visualization

This book presents methods and protocols for both fixed and live cells from everything from bacteria to mammalian models, offering detailed techniques from experts in the field. The text includes vital notes on troubleshooting and avoiding known pitfalls.

With its complex and extensively regulated metabolism, the study of the RNA lifecycle demands tools that allow for the localization of RNAs to be observed either in an in situ setting or, preferably, under in vivo conditions. In RNA Detection and Visualization: Methods and Protocols , the best and brightest investigators provide an up-to-date and in-depth description of basic methods and protocols used for detecting and visualizing mRNAs in both fixed and live cells, from bacteria to mammals. For novices and experts alike, this mix of classic in situ hybridization and advanced live imaging techniques, cell fractionation and affinity purification procedures, and bioinformatics tools gives researchers the most complete and extensive array of research aids possible. As a volume written in the highly successful Methods in 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 expert tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, RNA Detection and Visualization: Methods and Protocols offers well-honed techniques in order to inspire researchers around the world to further our knowledge of the vital biological significance of RNA.

Features methods and protocols relevant for both fixed and live cells from everything from bacteria to mammalian models Provides detailed techniques from established and up-and-coming experts in the field Includes vital notes on troubleshooting and avoiding known pitfalls for easier implementation of the methods

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Single Molecule Imaging of RNA In situ.- FISH and Immunofluorescence Staining in Chlamydomonas .- High Resolution Fluorescent In situ Hybridization in Drosophila.- Localization and Anchorage of Maternal mRNAs to Cortical Structures of Ascidian Eggs and Embryos Using High Resolution In situ Hybridization.- Visualization of mRNA Localization in Xenopus Oocytes.- Visualization of mRNA Expression in the Zebrafish Embryo.- High-Resolution Fluorescence In situ Hybridization to Detect mRNAs in Neuronal Compartments In vitro and In vivo.- Localization of mRNA in Vertebrate Axons Using In situ Hybridization.- Tiny Molecular Beacons for In vivo mRNA Detection.- Delivery of Molecular Beacons for Live-Cell Imaging and Analysis of RNA.- Genetically-Encoded Fluorescent Probes for Imaging Endogenous mRNA in Living Cells.- Visualization of Induced RNA in Single Bacterial Cells.- Visualizing mRNAs in Fixed and Living Yeast Cells.- In vivo Visualization of RNA Using the U1A-Based Tagged RNA System.- Visualizing Endogenous mRNAs in Living Yeast Using m-TAG, a PCR-Based RNA Aptamer Integration Method, and Fluorescence Microscopy.- Imaging mRNAs in Living Mammalian Cells.- Using the mRNA-MS2/MS2CP-FP System to Study mRNA Transport during Drosophila Oogenesis.- Genome-Wide Analysis of RNA Extracted from Isolated Mitochondria.- Analyzing mRNA Localization to the Endoplasmic Reticulum via Cell Fractionation.- Isolation of mRNAs Encoding Peroxisomal Proteins from Yeast Using a Combined Cell Fractionation and Affinity Purification Procedure.- Profiling Axonal mRNA Transport.- RNA Purification from Tumor Cell Protrusions Using Porous Polycarbonate Filters.-RNA-Binding Protein Immunopurification-Microarray (RIP-Chip) Analysis to Profile Localized RNAs.- RaPID: An Aptamer-Based mRNA Affinity Purification Technique for the Identification of RNA and Protein Factors Present in Ribonucleoprotein Complexes.- RIP: An mRNA Localization Technique.- The Dual Use of RNA Aptamer Sequences for Affinity Purification and Localization Studies of RNAs and RNA-Protein Complexes.- Identifying and Searching for Conserved RNA Localization Signals.- Computational Prediction of RNA Structural Motifs Involved in Post Transcriptional Regulatory Processes.