RNA Tagging

1. Front Matter

   Pages i-xiv

   PDF

2. In Situ Detection of RNA Molecules Using FISH Techniques

   1. Front Matter

      Pages 1-1

      PDF

   2. Tagging and Application of RNA Probes for Sequence-Specific Visualization of RNAs by Fluorescent In Situ Hybridization

      • Thomas Dresselhaus, Andrea Bleckmann

      Pages 3-21

   3. Quantitative Fluorescence In Situ Hybridization Detection of Plant mRNAs with Single-Molecule Resolution

      • Kun Huang, Mona Batish, Chong Teng, Alex Harkess, Blake C. Meyers, Jeffrey L. Caplan

      Pages 23-33

   4. Visualization of Endoplasmic Reticulum-Associated mRNA in Mammalian Cells

      • Jingze J. Wu, Alexander F. Palazzo

      Pages 35-49

   5. Simultaneous Detection of mRNA and Protein in S. cerevisiae by Single-Molecule FISH and Immunofluorescence

      • Evelina Tutucci, Robert H. Singer

      Pages 51-69

3. In Vivo Imaging of RNA Transport and Localization

   1. Front Matter

      Pages 71-71

      PDF

   2. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

      • Michael Ryckelynck

      Pages 73-102

   3. Visualization of Transiently Expressed mRNA in Plants Using MS2

      • Eduardo José Peña, Manfred Heinlein

      Pages 103-120

   4. New Generations of MS2 Variants and MCP Fusions to Detect Single mRNAs in Living Eukaryotic Cells

      • Xavier Pichon, Marie-Cécile Robert, Edouard Bertrand, Robert H. Singer, Evelina Tutucci

      Pages 121-144

   5. In Vivo Imaging of Mobile mRNAs in Plants Using MS2

      • Kai-Ren Luo, Nien-Chen Huang, Tien-Shin Yu

      Pages 145-155

   6. RNA Imaging with RNase-Inactivated Csy4 in Plants and Filamentous Fungi

      • David Burnett, Alexander Lichius, Jens Tilsner

      Pages 157-178

4. Imaging and Analysis of RNA Uptake and Transport Between Cells

   1. Front Matter

      Pages 179-179

      PDF

   2. Utilizing Potato Virus X to Monitor RNA Movement

      • Zhiming Yu, Sung Ki Cho, Pengcheng Zhang, Yiguo Hong, David J. Hannapel

      Pages 181-194

   3. A Protocol for Non-biased Identification of RNAs Transferred Between Heterologous Mammalian Cell Types Using RNA Tagging, Cell Sorting, and Sequencing

      • Sandipan Dasgupta, Jeffrey E. Gerst

      Pages 195-214

   4. Synthesizing Fluorescently Labeled dsRNAs and sRNAs to Visualize Fungal RNA Uptake

      • Rachael Hamby, Ming Wang, Lulu Qiao, Hailing Jin

      Pages 215-225

   5. Labeling of dsRNA for Fungal Uptake Detection Analysis

      • Matteo Galli, Jafargholi Imani, Karl-Heinz Kogel

      Pages 227-238

5. Identification and Analysis of RNA-Binding Proteins

   1. Front Matter

      Pages 239-239

      PDF

   2. Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs)

      • Mengge Shan, Brian D. Gregory

      Pages 241-253

   3. Plant Individual Nucleotide Resolution Cross-Linking and Immunoprecipitation to Characterize RNA-Protein Complexes

      • Tino Köster, Dorothee Staiger

      Pages 255-267

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.

• RNA-binding proteins
• RNA transport
• RNA-mediated editing
• CRISPR
• Guide RNA design
• Functional RNA complexes

• Institut de Biologie Moléculaire des Plantes (IBMP-CNRS), Université de Strasbourg, Strasbourg, France

  Manfred Heinlein

Policies and ethics