RNA Detection: Methods and Protocols

Front Matter ....Pages i-xiv
 The Secret Life of RNA: Lessons from Emerging Methodologies  (Caroline Medioni, Florence Besse)....Pages 1-28
 Quantification of 2′-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)  (Lilia Ayadi, Yuri Motorin, Virginie Marchand)....Pages 29-48
 Identifying the m6A Methylome by Affinity Purification and Sequencing  (Phillip J. Hsu, Chuan He)....Pages 49-57
 PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution  (Zhipeng Lu, Jing Gong, Qiangfeng Cliff Zhang)....Pages 59-84
 Axon-TRAP-RiboTag: Affinity Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo  (Toshiaki Shigeoka, Jane Jung, Christine E. Holt, Hosung Jung)....Pages 85-94
 LCM-Seq: A Method for Spatial Transcriptomic Profiling Using Laser Capture Microdissection Coupled with PolyA-Based RNA Sequencing  (Susanne Nichterwitz, Julio Aguila Benitez, Rein Hoogstraaten, Qiaolin Deng, Eva Hedlund)....Pages 95-110
 Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas  (Kaia Achim, Hernando Martínez Vergara, Jean-Baptiste Pettit)....Pages 111-125
 Single mRNA Molecule Detection in Drosophila  (Shawn C. Little, Thomas Gregor)....Pages 127-142
 Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos  (L. Carine Stapel, Coleman Broaddus, Nadine L. Vastenhouw)....Pages 143-162
 Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction  (Joshua S. Titlow, Lu Yang, Richard M. Parton, Ana Palanca, Ilan Davis)....Pages 163-175
 Detection of mRNA and Associated Molecules by ISH-IEM on Frozen Sections  (Catherine Rabouille)....Pages 177-186
 Hybridization Chain Reaction for Direct mRNA Detection Without Nucleic Acid Purification  (Yao Xu, Zhi Zheng)....Pages 187-196
 In Situ Detection of MicroRNA Expression with RNAscope Probes  (Viravuth P. Yin)....Pages 197-208
 Padlock Probes to Detect Single Nucleotide Polymorphisms  (Tomasz Krzywkowski, Mats Nilsson)....Pages 209-229
 Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons  (Yantao Yang, Mingming Chen, Christopher J. Krueger, Andrew Tsourkas, Antony K. Chen)....Pages 231-242
 Optimizing Molecular Beacons for Intracellular Analysis of RNA  (Mingming Chen, Yantao Yang, Christopher J. Krueger, Antony K. Chen)....Pages 243-257
 Live Imaging of Nuclear RNPs in Mammalian Complex Tissue with ECHO-liveFISH  (Dan Ohtan Wang)....Pages 259-272
 In Vivo Visualization and Function Probing of Transport mRNPs Using Injected FIT Probes  (Jasmine Chamiolo, Imre Gaspar, Anne Ephrussi, Oliver Seitz)....Pages 273-287
 Visualizing RNA in Live Bacterial Cells Using Fluorophore- and Quencher-Binding Aptamers  (Murat Sunbul, Ankita Arora, Andres Jäschke)....Pages 289-304
 Method for Imaging Live-Cell RNA Using an RNA Aptamer and a Fluorescent Probe  (Shin-ichi Sato, Kenji Yatsuzuka, Yousuke Katsuda, Motonari Uesugi)....Pages 305-318
 RNA Live Imaging in the Model Microorganism Ustilago maydis  (Sabrina Zander, Kira Müntjes, Michael Feldbrügge)....Pages 319-335
 Real-Time Fluorescence Imaging of Single-Molecule Endogenous Noncoding RNA in Living Cells  (Hideaki Yoshimura, Takeaki Ozawa)....Pages 337-347
 Live Imaging of mRNA Synthesis in Drosophila  (Hernan G. Garcia, Thomas Gregor)....Pages 349-357
 Imaging Newly Transcribed RNA in Cells by Using a Clickable Azide-Modified UTP Analog  (Anupam A. Sawant, Sanjeev Galande, Seergazhi G. Srivatsan)....Pages 359-371
 Detection of the First Round of Translation: The TRICK Assay  (Franka Voigt, Jan Eglinger, Jeffrey A. Chao)....Pages 373-384
 Imaging Translation Dynamics of Single mRNA Molecules in Live Cells  (Suzan Ruijtenberg, Tim A. Hoek, Xiaowei Yan, Marvin E. Tanenbaum)....Pages 385-404
 Systematic Detection of Poly(A)+ RNA-Interacting Proteins and Their Differential Binding  (Miha Milek, Markus Landthaler)....Pages 405-417
 Isolation and Characterization of Endogenous RNPs from Brain Tissues  (Rico Schieweck, Foong yee Ang, Renate Fritzsche, Michael A. Kiebler)....Pages 419-426
 Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein–RNA Interactions  (Christopher R. Sibley)....Pages 427-454
 RNA Tagging: Preparation of High-Throughput Sequencing Libraries  (Christopher P. Lapointe, Marvin Wickens)....Pages 455-471
 RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells  (Colleen A. McHugh, Mitchell Guttman)....Pages 473-488
Back Matter ....Pages 489-492