Lin R.-J. (Ed.) RNA-Protein Complexes and Interactions. Methods and Protocols

Humana Press, 2016 — 288p. — (Methods in Molecular Biology 1421) — ISBN: 978-1-4939-3591-8 (eBook), 978-1-4939-3589-5 (Hardcover).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.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