RNA-Protein Complexes and Interactions

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. Authoritative and up-to-date, RNA-Protein Complexes and Interactions: Methods and Protocols provides a set of useful protocols, both basic and advanced, designed to inspire researchers working with RNA and RNA-interacting proteins.

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

Inhalt
Characterization of RNA-Protein Interactions: Lessons from Two RNA-Binding Proteins, SRSF1 and SRSF2.- Identification of mRNA-Interacting Factors by MS2-TRAP (MS2-Tagged RNA Affinity Purification).- Biotin-Streptavidin Affinity Purification of RNA-Protein Complexes Assembled In Vitro.- Detecting RNA-Protein Interaction Using End-Labeled Biotinylated RNA Oligonucleotides and Immunoblotting.- Purification of RNA-Protein Splicing Complexes Using a Tagged Protein from In Vitro Splicing Reaction Mixture.- Loading of Argonaute Protein with Small Duplex RNA in Cellular Extracts.- In Vitro Analysis of Ribonucleoprotein Complex Remodeling and Disassembly.- Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases.- Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles.- Northwestern Blot Analysis: Detecting RNA-Protein Interaction After Gel Separation of Protein Mixture.- Measuring mRNA Translation by Polysome Profiling.- Genome-Wide Profiling of RNA-Protein Interactions Using CLIP-Seq.- Identification of Endogenous mRNA-Binding Proteins in Yeast Using Crosslinking and PolyA Enrichment.- Ribo-Proteomics Approach to Profile RNA-Protein and Protein-Protein Interaction Networks.- Detection of Protein-Protein Interaction Within an RNA-Protein Complex Via Unnatural-Amino-Acid-Mediated Photochemical Crosslinking.- Evolution of Cell-Type-Specific RNA Aptamers Via Live Cell-Based SELEX.- mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA Binding Proteins.- Design of RNA-Binding Proteins: Manipulate Alternative Splicing in Human Cells with Artificial Splicing Factors.- Informational Suppression to Probe RNA:RNA Interactions in the Context of Ribonucleoproteins: U1 and 5' Splice-Site Base-Pairing.- Analysis of Alternative Pre-RNA Splicing in the Mouse Retina Using a Fluorescent Reporter.