RNA detection and visualization : methods and protocols / edited by Jeffrey E. Gerst. — [Totowa, N.J.] : Humana, c2011. – (58.17/M592/v.714)

Contents

        CONTENTS
    
    PART I VISUALIZING MRNAs IN SITU
    1 Single Molecule Imaging of RNA In Situ
    2 FISH and Immunofluorescence Staining in Chlamydomonas
    3 High Resolution Fluorescent In Situ Hybridization in Drosophila 31
    4 Localization and Anchorage of Maternal mRNAs to Cortical Structures of Ascidian Eggs and Embryos Using High Resolution In Situ Hybridization
    5 Visualization of mRNA Localization in Xenopus Oocytes
    6 Visualization of mRNA Expression in the Zebrafish Embryo
    7 High-Resolution Fluorescence In Situ Hybridization to Detect mRNAs in Neuronal Compartments In Vitro and In Vivo 103
    8 Localization of mRNA in Vertebrate Axonal Compartments by In Situ Hybridization
    PART II VISUALIZING MRNAs IN VIVO USING MOLECULAR PROBES OR RECONSTITUTED FLUORESCENT PROTEINS
    9 Tiny Molecular Beacons for in vivo mRNA Detection 141
    10 Delivery of Molecular Beacons for Live-Cell Imaging and Analysis of RNA 159
    11 Genetically-Encoded Fluorescent Probes for Imaging Endogenous mRNA in Living Cells
    12 Visualization of Induced RNA in Single Bacterial Cells
    PART III VISUALIZING MRNAs IN VIVO USING APTAMERS AND INTACT FLUORESCENT PROTEINS
    13 Visualizing mRNAs in Fixed and Living Yeast Cells
    14 In Vivo Visualization of RNA Using the U1A-Based Tagged RNA System
    15 Visualizing Endogenous mRNAs in Living Yeast Using m-TAG， a PCR-Based RNA Aptamer Integration Method， and Fluorescence Microscopy 237
    16 Imaging mRNAs in Living Mammalian Cells
    17 Using the mRNA-MS2/MS2CP-FP System to Study mRNA Transport During Drosophila Oogenesis
    PART IV USE OF CELL FRACTIONATION TO DEMONSTRATE THE SUB-CELLULAR LOCALIZATION OF RNA
    18 Genome-Wide Analysis of RNA Extracted from Isolated Mitochondria 287
    19 Analyzing mRNA Localization to the Endoplasmic Reticulum via Cell Fractionation
    20 Isolation of mRNAs Encoding Peroxisomal Proteins from Yeast Using a Combined Cell Fractionation and Affinity Purification Procedure
    21 Profiling Axonal mRNA Transport
    22 RNA Purification from Tumor Cell Protrusions Using Porous Polycarbonate Filters
    PART V AFFINITY PURIFICATION OF MRNAs AND THE IDENTIFICATION OF TRA Ns-ACTING FACTORS
    23 RNA-Binding Protein Immunopurification-Microarray (RIP-Chip) Analysis to Profile Localized RNAs
    24 RAPID: An Aptamer-Based mRNA Affinity Purification Technique for the Identifcation of RNA and Protein Factors Present in Ribonucleoprotein Complexes
    25 RIP: An mRNA Localization Technique
    26 The Dual Use of RNA Aptamer Sequences for Affinity Purification and Localization Studies of RNAs and RNA-Protcin Complexes 423
    PART VI USE OF BIOINFORMATICS TO IDENTIFY C/S-ACTING MOTIFS AND STRUCTURES IN RNAs
    27 Identifying and Searching for Conserved KNA Localisation Signals 447
    28 Computational Prediction of RNA Structural Motifs Involved in Post-Transcriptional Regulatory Processes 467
    Index 481