RNA Tagging: Methods and Protocols

ISBN-13: 9781071607114 / Angielski / Twarda / 2020 / 490 str.

Manfred Heinlein

Spis treści

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 José Peña and Manfred Heinlein

 

7. 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, 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 Köster 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 Böhrer, 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

            Stéphanie Lalande, Marjorie Chery, Elodie Ubrig, Guillaume Hummel, Julie Kubina, Angèle Geldreich, and Laurence Drouard

 

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

            Károly Fátyol

 

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

            Soledad Traubenik, Flavio Blanco, María 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

Blurb

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.