RNA Remodeling Proteins

This third edition provides new and updated methods for the further study of RNA remodeling proteins. Chapters detail RNA remodeling proteins, AlphaFold to RNA-protein complexes, deep sequencing to probe transcriptome-wide remodeling events, helicase-dependent RNA structural changes, identifying helicase substrates, mapping transcriptional R-loops, leveraging techniques such as RNA-seq, DMS-seq, CLIP-seq, H-CRAC, Helicase-SELEX, proximity ligation, yeast three-hybrid assays, biochemical assays to measure RNA-protein affinity and helicase activities, structural and biophysical methods, an d functional characterization of RNA remodeling proteins. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, RNA Remodeling Proteins: Methods and Protocols, Third Edition aims to ensure successful results in the further study of this vital field.

Key points to consider when studying RNA remodeling by proteins. - Predicting RNA and protein:RNA complexes with AlphaFold: possibilities, limitations, and practical guidelines. - Guidelines to study transcriptome remodeling by proteins using deep sequencing (RNA-seq). - Tools for experimental and computational genome-wide analysis of the function of DDX5 and DDX17 helicases in RNA processing. - A Workflow for Identifying Helicase-Dependent RNA Structural Changes in Transcriptional Termination: From DMS Sequencing Analysis to Reporter Assay-Based Validation. - Using cross-linking and immunoprecipitation (CLIP) to identify targets and specificity determinants of the YTHDC2 helicase. - Genome-wide mapping of R-loops in S. cerevisiae by H-CRAC. - Global identification of RNA helicase substrates from large nucleic acid sequence libraries using Helicase-SELEX. - Identification of host interaction partners of the Hepatitis E Virus Internal Ribosome Entry Site like-RNA using RNA-protein interaction detection assay and yeast three-hybrid assay. - Purification of C/D-box snoRNP and fibrillarin associated factors from Arabidopsis thaliana plants using GFP-tagged proteins. - In Vitro RNA Protein Binding Assays to Identify RNA Helicases for U snRNA Nuclear Export. - Quantifying Label-Free Protein RNA Binding Using Microscale Thermophoresis. - Measuring the affinity of the bacterial Rho helicase for RNA using a double membrane slot-blot filtration assay. - Unwinding Quadruplex Structures with RNA Helicases. - Insights into the activities of helicases from Thermococcales: the cases of the RNA helicase ASH-Ski2, the DNA helicase Hel308 and the RNA:DNA helicase Lhr2. - Mapping of RNA helicase dynamics by HDX-MS. - Native Liquid MALDI (NALIM) mass spectrometry analysis of RNA-binding protein complexes. - Using solution NMR to study the RNA-binding properties and molecular mechanisms of the RNA helicase DDX3X. - Using magnetic tweezers to unravel the mechanism of the G-quadruplex binding and unwinding activities of DHX36 helicase. - In vitro assay of bacterial RNA helicases liquid-liquid phase separation. - Probing the role of RNA helicases in modulating stress granules, RNA localization and P-body docking. - Fast analysis of RNA from transcription and Rho-dependent termination assays using automated capillary electrophoresis. - Assays to study SUMOylation of RNA helicase DHX9. - Analysis of Bacillus subtilis ribonuclease activity in vivo. - Assay of Bacillus subtilis ribonuclease activity in vitro.