RNA-Protein Complexes and Interactions: Methods and Protocols

ISBN-13: 9781071631904 / Angielski

Ren-Jang Lin

Opis

This second edition updates, complements, and expands upon the first edition by providing a collection of cutting-edge techniques developed or refined in the past few years along with tried-and-true methods. Chapters explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.Authoritative and cutting-edge, RNA-Protein Complexes and Interactions: Methods and Protocols, Second Edition aims to be comprehensive guide for researchers in the field.

Spis treści

1. In vivo cross-linking and co-immunoprecipitation procedure to analyze nuclear tRNA export complexes in yeast cells

Kunal Chatterjee and Anita K. Hopper

 

2. Analysis of Gene Expression Patterns and RNA Localization by Fluorescence in situ Hybridization in Whole Mount Drosophila Testes

Jaclyn M. Fingerhut and Yukiko M. Yamashita

 

3. Electrophoretic mobility shift assay (EMSA) and microscale thermophoresis (MST) methods to measure interactions between tRNAs and their modifying enzymes

Andrzej Chramiec-Głąbik, Michał Rawski, Sebastian Glatt and Ting-Yu Lin

 

4. Mapping of RNase P ribozyme regions in proximity with a human RNase P subunit protein using Fe(II)-EDTA cleavage and nuclease footprint analyses

Phong Trang, Adam Smith, and Fenyong Liu

 

5. SHAPE to probe RNA structure and RNA-protein interactions in vitro

Kaushik Saha and Gourisankar Ghosh

 

6. Chemical probing of RNA structure in vivo using SHAPE-MaP and DMS-MaP

Kaushik Saha and Gourisankar Ghosh

 

7. Analysis of RNA-protein interaction networks using RNP-MaP

Kaushik Saha and Gourisankar Ghosh

 

8. Native RNA immunoprecipitation (RIP) for precise detection and quantification of protein-interacting RNA

Mai Baker, Rami Khosravi, and Maayan Salton

 

9. In vivo cross-linking and co-immunoprecipitation procedure to analyze nuclear tRNA export complexes in yeast cells

Kunal Chatterjee and Anita K. Hopper

 

10. Identify microRNA targets using AGO2-CLASH (Cross-linking, Ligation, And Sequencing of Hybrids) and AGO2-CLIP (Cross-Linking and Immuno-Precipitation) in cells with or without the microRNA of interest depleted

Mitsuo Kato

 

11. Ribosomal Profiling by Gradient Fractionation of Cell Lysates

Nimisha Bhattarai, Bo Cao, Shelya X Zeng, and Hua Lu

 

12. Global assessment of protein translation in mammalian cells using polysome fractionation

Jingrong Zhao and Sika Zheng

 

13. Fluorescent in situ detection of RNA-Protein interactions in intact cells by RNA-PLA

Tianqi Li, Wei Zhang, and Mingyi Xie

14. In vitro reconstitution of pseudouridylation catalyzed by human box H/ACA ribonucleoprotein particles

Hironori Adachi, Jonathan L. Chen, Qiangzong Yin, Pedro Morais,  and Yi-Tao Yu

 

15. Arresting Spliceosome Intermediates at Various Stages of the Splicing Pathway

Chi-Kang Tseng and Soo-Chen Cheng

 

16. Streamlined purification of RNA-protein complexes using UV crosslinking and RNA antisense purification

Nhu Trang, Tong Su, Simone Hall, Nada Boutros, Bobby Kong, Calvin Huang, and Colleen A. McHugh

 

17. MS2-MBP based affinity purification of nucleus- or cytoplasm-localized lncRNA-protein complexes formed in vivo

Shuai Hou, Weijie Wang, Tian Hao, and Haixin Lei

 

18. RNA and protein interactomes of an RNA-binding protein tagged with FLAG epitopes using combinatory approaches of genome engineering and stable transfection

Sze Cheng, Meeyeon Park, and Jeongsik Yong

 

19. Detecting R-loop formation using a plasmid-based in vitro transcription assay

Lei Shen and Yanzhong Yang

 

20. Methods to Study RNA-Chromatin Interactions

Kiran Sriram, Yingjun Luo, Naseeb K Malhi, Aleysha Chen,  and Zhen Bouman Chen

 

21. Challenges for Studying and Isolating Extracellular Vesicles from Cell-conditioned Media

Andrew R. Chin

22. Evolution of Cell-Type-Specific RNA Aptamers Via Live Cell-Based SELEX

Alberto Herrera, Jiehua Zhou, Min-sun Song, and John J. Rossi