RNA Detection and Visualization

Methods and Protocols

Editors:

ISBN: 978-1-61779-004-1 (Print) 978-1-61779-005-8 (Online)

Table of contents (28 protocols)

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  1. Front Matter

    Pages i-xiv

  2. Visualizing mRNAs In Situ

    1. Front Matter

      Pages 1-1

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      Pages 3-13

      Single Molecule Imaging of RNA In Situ

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      Pages 15-29

      FISH and Immunofluorescence Staining in Chlamydomonas

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      Pages 31-47

      High Resolution Fluorescent In Situ Hybridization in Drosophila

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      Pages 49-70

      Localization and Anchorage of Maternal mRNAs to Cortical Structures of Ascidian Eggs and Embryos Using High Resolution In Situ Hybridization

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      Pages 71-82

      Visualization of mRNA Localization in Xenopus Oocytes

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      Pages 83-102

      Visualization of mRNA Expression in the Zebrafish Embryo

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      Pages 103-123

      High-Resolution Fluorescence In Situ Hybridization to Detect mRNAs in Neuronal Compartments In Vitro and In Vivo

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      Pages 125-138

      Localization of mRNA in Vertebrate Axonal Compartments by In Situ Hybridization

  3. Visualizing mRNAs In Vivo Using Molecular Probes or Reconstituted Fluorescent Proteins

    1. Front Matter

      Pages 139-139

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      Pages 141-157

      Tiny Molecular Beacons for in vivo mRNA Detection

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      Pages 159-174

      Delivery of Molecular Beacons for Live-Cell Imaging and Analysis of RNA

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      Pages 175-188

      Genetically-Encoded Fluorescent Probes for Imaging Endogenous mRNA in Living Cells

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      Pages 189-199

      Visualization of Induced RNA in Single Bacterial Cells

  4. Visualizing mRNAs In Vivo Using Aptamers and Intact Fluorescent Proteins

    1. Front Matter

      Pages 201-201

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      Pages 203-219

      Visualizing mRNAs in Fixed and Living Yeast Cells

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      Pages 221-235

      In Vivo Visualization of RNA Using the U1A-Based Tagged RNA System

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      Pages 237-247

      Visualizing Endogenous mRNAs in Living Yeast Using m-TAG, a PCR-Based RNA Aptamer Integration Method, and Fluorescence Microscopy

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      Pages 249-263

      Imaging mRNAs in Living Mammalian Cells

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      Pages 265-283

      Using the mRNA-MS2/MS2CP-FP System to Study mRNA Transport During Drosophila Oogenesis

  5. Use of Cell Fractionation to Demonstrate the Sub-Cellular Localization of RNA

    1. Front Matter

      Pages 285-285

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      Pages 287-299

      Genome-Wide Analysis of RNA Extracted from Isolated Mitochondria

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      Pages 301-321

      Analyzing mRNA Localization to the Endoplasmic Reticulum via Cell Fractionation

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      Pages 323-333

      Isolation of mRNAs Encoding Peroxisomal Proteins from Yeast Using a Combined Cell Fractionation and Affinity Purification Procedure

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