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RNA Tagging
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Table of Contents

Part I: In Situ Detection of RNA Molecules Using FISH Techniques 1. Tagging and Application of RNA Probes for Sequence-Specific Visualization of RNAs by Fluorescent In Situ Hybridization

Thomas Dresselhaus and Andrea Bleckmann

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

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

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

Jingze J. Wu and Alexander F. Palazzo

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

Evelina Tutucci and Robert H. Singer

Part II: In Vivo Imaging of RNA Transport and Localization 5. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

Michael Ryckelynck

6. Visualization of Transiently Expressed mRNA in Plants Using MS2

Eduardo Jose Pena and Manfred Heinlein

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

Xavier Pichon, Marie-Cecile Robert, Edouard Bertrand, Robert H. Singer, and Evelina Tutucci

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

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

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

David Burnett, Alexander Lichius, and Jens Tilsner

Part III: Imaging and Analysis of RNA Uptake and Transport between Cells 10. Utilizing Potato Virus X to Monitor RNA Movement

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

11. A Protocol for Non-Biased Identification of RNAs Transferred between Heterologous Mammalian Cell Types Using RNA Tagging, Cell Sorting, and Sequencing

Sandipan Dasgupta and Jeffrey E. Gerst

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

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

13. Labeling of dsRNA for Fungal Uptake Detection Analysis

Matteo Galli, Jafargholi Imani, and Karl-Heinz Kogel

Part IV: Identification and Analysis of RNA-Binding Proteins 14. Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs)

Mengge Shan and Brian D. Gregory

15. Plant Individual Nucleotide Resolution Crosslinking and Immunoprecipitation to Characterize RNA-Protein Complexes

Tino Koester and Dorothee Staiger

16. A Single-Molecule RNA Mobility Assay to Identify Proteins that Link RNAs to Molecular Motors

Varun Bhaskar, Min Jia, and Jeffrey A. Chao

17. Proximity-CLIP Provides a Snapshot of Protein-Occupied RNA Elements at Subcellular Resolution and Transcriptome-Wide Scale

Daniel Benhalevy and Markus Hafner

18. Double-Stranded RNA Pull-Down to Characterize Viral Replication Complexes in Plants

Marco Incarbone and Christophe Ritzenthaler

Part V: RNAs as Guides for Genome Editing and Imaging of Chromosome Loci 19. CRISPR Guide RNA Design Guidelines for Efficient Genome Editing

Patrick Schindele, Felix Wolter, and Holger Puchta

20. Live Cell CRISPR Imaging in Plant Cells with a Telomere-Specific Guide RNA Solmaz Khosravi, Steven Dreissig, Patrick Schindele, Felix Wolter, Twan Rutten, Holger Puchta, and Andreas Houben 21. Live-Cell Imaging of Genomic Loci Using CRISPR/Molecular Beacon Hybrid Systems

Xiaotian Wu, Yachen Ying, Shiqi Mao, Christopher J. Krueger, and Antony K. Chen

22. Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos

Hongtao Chen and Thomas Gregor

Part VI: Specific Techniques for the Analysis of RNA Functions 23. Integrated Genome-Scale Analysis and Northern Blot Detection of Retrotransposon siRNAs across Plant Species

Marcel Bo hrer, Bart Rymen, Christophe Himber, Aude Gerbaud, David Pflieger, Debbie Laudencia-Chingcuanco, Amy Cartwright, John Vogel, Richard Sibout, and Todd Blevins

24. Transfection of Small Non-Coding RNAs into Arabidopsis thaliana Protoplasts

Stephanie Lalande, Marjorie Chery, Elodie Ubrig, Guillaume Hummel, Julie Kubina, Angele Geldreich, and Laurence Drouard

25. In Vivo Reporter System for miRNA-Mediated RNA Silencing

Karoly Fatyol

26. TRAP-SEQ of Eukaryotic Translatomes Applied to the Detection of Polysome-Associated Long Non-Coding RNAs

Soledad Traubenik, Flavio Blanco, Maria Eugenia Zanetti, and Mauricio A. Reynoso

27. Posttranscriptional Suzuki-Miyaura Cross-Coupling Yields Labeled RNA for Conformational Analysis and Imaging

Manisha B. Walunj and Seergazhi G. Srivatsan

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