Main description:

This volume introduces different concepts and methods of detecting RNA in biological material in a variety of model systems. The chapters in this book discuss methods that will answer numerous biological questions that arise in the study of RNAs. Some of the topics covered in this book are single mRNA molecule detection in embryos and neurons; detection of mRNA and associated molecules by ISH-IEM on frozen sections; optimizing molecular beacons for intracellular analysis of RNA; imaging translation dynamics of single mRNA molecules in live cells; preparation of high-throughput sequencing libraries; and capturing RNA binding proteins in embryos and in cell-culture. Written in the highly successful Methods in Molecular Biology series format, 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.

Cutting-edge and comprehensive, RNA Detection: Methods and Protocols is a valuable resource for novel and experiences scientist in the expanding field of RNAs.

Contents:

Preface...
Table of Contents...
Contributing Authors...

1. The Secret Life of RNA: Lessons from Emerging Methodologies
Caroline Medioni and Florence Besse
2. Quantification of 2'-O-Me Residues in RNA using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
Lilia Ayadi, Yuri Motorin, and Virginie Marchand

3. Identifying the m6A Methylome by Affinity Purification and Sequencing
Phillip J. Hsu and Chuan He

4. PARIS: Psoralen Analysis of RNA Interactions and Structures with High Throughput and Resolution
Zhipeng Lu, Jing Gong, and Qiangfeng Cliff Zhang

5. Axon-TRAP-RiboTag: Affinity-Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo
Toshiaki Shigeoka, Jane Jung, Christine E. Holt, and Hosung Jung

6. 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, and Eva Hedlund

7. Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas
Kaia Achim, Hernando Martinez Vergara, and Jean-Baptiste Pettit

8. Single mRNA Molecule Detection in Drosophila
Shawn C. Little and Thomas Gregor

9. Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos
L. Carine Stapel, Coleman Broaddus, and Nadine L. Vastenhouw

10. Super-Resolution Single Molecule FISH at the Drosophila Neuromuscular Junction
Joshua S. Titlow, Lu Yang, Richard M. Parton, Ana Palanca, and Ilan Davis

11. Detection of mRNA and Associated Molecules by ISH-IEM on Frozen Sections
Catherine Rabouille

12. Hybridization Chain Reaction for Direct mRNA Detection without Nucleic Acid Purification
Yao Xu and Zhi Zheng

13. In Situ Detection of MicroRNA Expression with RNAscope Probes
Viravuth P. Yin

14. Padlock Probes to Detect Single Nucleotide Polymorphisms
Tomasz Krzywkowski and Mats Nilsson

15. Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons
Yantao Yang, Mingming Chen, Christopher K. Krueger, Andrew Tsourkas, and Antony K. Chen

16. Optimizing Molecular Beacons for Intracellular Analysis of RNA
Mingming Chen, Yantao Yang, Christopher K. Krueger, and Antony K. Chen

17. Live Imaging of Nuclear RNPs in Mammalian Complex Tissue with ECHO-liveFISH
Dan Ohtan Wang

18. In Vivo Visualization and Function Probing of Transport mRNPs using Injected FIT Probes
Jasmine Chamiolo, Imre Gaspar, Anne Ephrussi, and Oliver Seitz

19. Visualizing RNA in Live Bacterial Cells using Fluorophore- and Quencher-Binding Aptamers
Murat Sunbul, Ankita Arora, and Andres Jaschke

20. Method for Imaging Live-Cell RNA using an RNA Aptamer and a Fluorescent Probe
Shin-ichi Sato, Kenji Yatsuzuka, Yousuke Katsuda, and Motonari Uesugi

21. RNA Live Imaging in the Model Microorganism Ustilago maydis
S. Zander, K. Muntjes, and M. Feldbrugge

22. Real-Time Fluorescence Imaging of Single-Molecule Endogenous Non-Coding RNA in Living Cells
Hideaki Yoshimura and Takeaki Ozawa

23. Live Imaging of mRNA Synthesis in Drosophila
Hernan G. Garcia and Thomas Gregor

24. Imaging Newly Transcribed RNA in Cells by Using a Clickable Azide-Modified UTP Analog
Anupam A. Sawant, Sanjeev Galande, and Seergazhi G. Srivatsan

25. Detection of the First Round of Translation: The TRICK Assay
Franka Voigt, Jan Eglinger, and Jeffrey A. Chao

26. Imaging Translation Dynamics of Single mRNA Molecules in Live Cells
Suzan Ruijtenberg, Tim A. Hoek, Xiaowei Yan, and Marvin E. Tanenbaum

27. Systematic Detection of Poly(A)+ RNA-Interacting Proteins and Their Differential Binding
Miha Milek and Markus Landthaler

28. Isolation and Characterization of Endogenous RNPs from Brain Tissues
Rico Schieweck, Foong yee Ang, Renate Fritzsche, and Michael A. Kiebler

29. Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein-RNA Interactions
Christopher R. Sibley

30. RNA Tagging: Preparation of High-Throughput Sequencing Libraries
Christopher P. Lapointe and Marvin Wickens

31. RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells
Colleen A. McHugh and Mitchell Guttman