RNA-Protein Complexes and Interactions, 1st ed. 2016 Methods and Protocols Methods in Molecular Biology Series, Vol. 1421

This detailed volume explores the continuing techniques of studying RNA-protein complexes and interactions as research in these areas expand.  After an introductory chapter, the book continues with ways to purify RNA-protein complexes assembled in cells or in isolated cellular extracts, methods for measuring various biochemical activities of RNA-interacting proteins or ribonucleoproteins, biochemical methods for measuring direct RNA-protein contact, as well as various new or innovative methods pertinent to the subject. Written for the highly successful Methods in Molecular Biology series, chapters contain brief 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.

1. Characterization of RNA-Protein Interactions: Lessons from Two RNA-Binding Proteins, SRSF1 and SRSF2

            Lindsey Skrdlant and Ren-Jang Lin

2. Identification of mRNA-Interacting Factors by MS2-TRAP (MS2-Tagged RNA Affinity Purification)

            Je-Hyun Yoon and Myriam Gorospe

3. Biotin-Streptavidin Affinity Purification of RNA-Protein Complexes Assembled In Vitro

            Shuai Hou, Lei Shi, and Haixin Lei

            Xuexiu Zheng, Sunghee Cho, Heegyum Moon, Tiing Jen Loh, Hana Jang, and Haihong Shen

5. Purification of RNA-Protein Splicing Complexes Using a Tagged Protein from In Vitro Splicing Reaction Mixture

            Naoyuki Kataoka

6. Loading of Argonaute Protein with Small Duplex RNA in Cellular Extracts

            Keith T. Gagnon

            Hua-Lin Zhou and Hua Lou

8. Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases

            Ya-Ming Hou

9. Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles

            Chao Huang, Guowei Wu, and Yi-Tao Yu

10. Northwestern Blot Analysis: Detecting RNA-Protein Interaction After Gel Separation of Protein Mixture

            Shangbing Zang and Ren-Jang Lin

11. Measuring mRNA Translation by Polysome Profiling

            Marek Kudla and Fedor V. Karginov

12. Genome-Wide Profiling of RNA-Protein Interactions Using CLIP-Seq

            Cheryl Stork and Sika Zheng

13. Identification of Endogenous mRNA-Binding Proteins in Yeast Using Crosslinking and PolyA Enrichment

14. Ribo-Proteomics Approach to Profile RNA-Protein and Protein-Protein Interaction Networks

            Hsin-Sung Yeh, Jae-Woong Chang, and Jeongsik Yong

15. Detection of Protein-Protein Interaction Within an RNA-Protein Complex Via Unnatural-Amino-Acid-Mediated Photochemical Crosslinking

            Fu-Lung Yeh, Luh Tung, and Tien-Hsien Chang

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

17. mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA Binding Proteins

            Sebastien M. Weyn-Vanhentenryck and Chaolin Zhang

18. Design of RNA-Binding Proteins: Manipulate Alternative Splicing in Human Cells with Artificial Splicing Factors

            Yang Wang and Zefeng Wang

19. Informational Suppression to Probe RNA:RNA Interactions in the Context of Ribonucleoproteins: U1 and 5’ Splice-Site Base-Pairing

            Jiazi Tan and Xavier Roca

20. Analysis of Alternative Pre-RNA Splicing in the Mouse Retina Using a Fluorescent Reporter

            Daniel Murphy, Saravanan Kolandaivelu, Visvanathan Ramamurthy, and Peter Stoilov

Includes cutting-edge methods and protocols for studying RNA-protein interactions

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras