CiNii 図書 - RNA tagging : methods and protocols

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.

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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RNA tagging : methods and protocols

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