Rna-Protein Complexes and Interactions: Methods and Protocols (Paperback)

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 4. Detecting RNA-Protein Interaction Using End-Labeled Biotinylated RNA Oligonucleotides and Immunoblotting 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 7. In Vitro Analysis of Ribonucleoprotein Complex Remodeling and Disassembly 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 Sarah F. Mitchell and Roy Parker 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 Jiehua Zhou and John J. Rossi 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