RNA Analysis: Methods and Protocols(2962 Methods in Molecular Biology)

This volume explores the latest technologies for RNA analysis, covering fundamental techniques and innovative approaches that expand our understanding of RNA biology. The chapters in this book are organized into four parts: reverse transcription and RNA capture methods; high-throughput sequencing methods; RNA maturation: splicing, polyadenylation, and epitranscriptomic modifications; and RNA surveillance: nonsense-mediated mRNA decay. These chapters aim to provide detailed protocols for select techniques used by molecular and computational biologists to isolate, amplify, detect, modify, and analyze RNA to gain insight into a wide range of cellular functions. Written in the highly successful Methods in Molecular Biology series format, chapters include 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. Cutting-edge and comprehensive, RNA Analysis: Methods and Protocols is a valuable resource for students, technicians, and senior scientists who want to learn more about this dynamic field of RNA research.

Table of Contents:
Guidelines for RNA Analysis by Reverse Transcription Quantitative Polymerase Chain Reaction.- Rare Transcripts Quantification by Strand Specific RT-qPCR.- Detection of Cancer Associated Gene Fusion by Ligation Dependent RT-PCR.- Isolation of a Specific Transcript Using Biotinylated Antisense Probes.- Transcriptome-Wide Characterization of Protein:RNA Interactions with UV-Crosslinking Immunoprecipitation and Sequencing.- Targeted 16S rRNA Gene Sequencing for Water Samples.- RNA-Based High-Throughput Sequencing of the Human Immunoglobulin Repertoire.- 5’RACE Method for RNA-Based Sequencing of the Mouse Immunoglobulin Repertoire.- A Wet Lab Procedure for Gene Fusion Analysis by Targeted RNA Next Generation Sequencing in Lung Cancer.- Simultaneous Profiling of Transcripts and Genomic Regions Associated with Nuclear Bodies using the RNA-DNA High-Salt Recovered Sequence (RD-HRS) Method.- Functional Evaluation of Splice Variants Using a Minigene Strategy.- Design and Evaluation of a Truncated Protein Induction Strategy by Antisense Oligonucleotide-Mediated Exon Skipping.- Modifying 3'-End RNA Isoforms using Antisense Oligonucleotides.- A Mass Spectrometry-Based Pipeline for Analyzing RNA Modifications in Cells and Tissues.- Inhibition of Nonsense-Mediated Decay in Dorsal Root Ganglion Neurons.- Knockdown of Gene Expression Following Activation of the NMD Pathway Using Splice-Switching Oligonucleotides.- Screening Methods for NMD Inhibitors or Readthrough Activators.