RNA Tagging: Methods and Protocols

Front Matter ....Pages i-xiv
Front Matter ....Pages 1-1
 Tagging and Application of RNA Probes for Sequence-Specific Visualization of RNAs by Fluorescent In Situ Hybridization  (Thomas Dresselhaus, Andrea Bleckmann)....Pages 3-21
 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
 Visualization of Endoplasmic Reticulum-Associated mRNA in Mammalian Cells  (Jingze J. Wu, Alexander F. Palazzo)....Pages 35-49
 Simultaneous Detection of mRNA and Protein in S. cerevisiae by Single-Molecule FISH and Immunofluorescence  (Evelina Tutucci, Robert H. Singer)....Pages 51-69
Front Matter ....Pages 71-71
 Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More  (Michael Ryckelynck)....Pages 73-102
 Visualization of Transiently Expressed mRNA in Plants Using MS2  (Eduardo José Peña, Manfred Heinlein)....Pages 103-120
 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
 In Vivo Imaging of Mobile mRNAs in Plants Using MS2  (Kai-Ren Luo, Nien-Chen Huang, Tien-Shin Yu)....Pages 145-155
 RNA Imaging with RNase-Inactivated Csy4 in Plants and Filamentous Fungi  (David Burnett, Alexander Lichius, Jens Tilsner)....Pages 157-178
Front Matter ....Pages 179-179
 Utilizing Potato Virus X to Monitor RNA Movement  (Zhiming Yu, Sung Ki Cho, Pengcheng Zhang, Yiguo Hong, David J. Hannapel)....Pages 181-194
 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
 Synthesizing Fluorescently Labeled dsRNAs and sRNAs to Visualize Fungal RNA Uptake  (Rachael Hamby, Ming Wang, Lulu Qiao, Hailing Jin)....Pages 215-225
 Labeling of dsRNA for Fungal Uptake Detection Analysis  (Matteo Galli, Jafargholi Imani, Karl-Heinz Kogel)....Pages 227-238
Front Matter ....Pages 239-239
 Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs)  (Mengge Shan, Brian D. Gregory)....Pages 241-253
 Plant Individual Nucleotide Resolution Cross-Linking and Immunoprecipitation to Characterize RNA-Protein Complexes  (Tino Köster, Dorothee Staiger)....Pages 255-267
 A Single-Molecule RNA Mobility Assay to Identify Proteins that Link RNAs to Molecular Motors  (Varun Bhaskar, Min Jia, Jeffrey A. Chao)....Pages 269-282
 Proximity-CLIP Provides a Snapshot of Protein-Occupied RNA Elements at Subcellular Resolution and Transcriptome-Wide Scale  (Daniel Benhalevy, Markus Hafner)....Pages 283-305
 Double-Stranded RNA Pull-Down to Characterize Viral Replication Complexes in Plants  (Marco Incarbone, Christophe Ritzenthaler)....Pages 307-327
Front Matter ....Pages 329-329
 CRISPR Guide RNA Design Guidelines for Efficient Genome Editing  (Patrick Schindele, Felix Wolter, Holger Puchta)....Pages 331-342
 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 et al.)....Pages 343-356
 Live-Cell Imaging of Genomic Loci Using CRISPR/Molecular Beacon Hybrid Systems  (Xiaotian Wu, Yachen Ying, Shiqi Mao, Christopher J. Krueger, Antony K. Chen)....Pages 357-372
 Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos  (Hongtao Chen, Thomas Gregor)....Pages 373-384
Front Matter ....Pages 385-385
 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 et al.)....Pages 387-411
 Transfection of Small Noncoding RNAs into Arabidopsis thaliana Protoplasts  (Stéphanie Lalande, Marjorie Chery, Elodie Ubrig, Guillaume Hummel, Julie Kubina, Angèle Geldreich et al.)....Pages 413-429
 In Vivo Reporter System for miRNA-Mediated RNA Silencing  (Károly Fátyol)....Pages 431-450
 TRAP-SEQ of Eukaryotic Translatomes Applied to the Detection of Polysome-Associated Long Noncoding RNAs  (Soledad Traubenik, Flavio Blanco, María Eugenia Zanetti, Mauricio A. Reynoso)....Pages 451-472
 Posttranscriptional Suzuki-Miyaura Cross-Coupling Yields Labeled RNA for Conformational Analysis and Imaging  (Manisha B. Walunj, Seergazhi G. Srivatsan)....Pages 473-486
Back Matter ....Pages 487-490