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This volume presents the most recent advances in techniques for studying the post-transcriptional regulation of gene expression (PTR). With sections on bioinformatics approaches, expression profiling, the protein and RNA interactome, the mRNA lifecycle, and RNA modifications, the book guides molecular biologists toward harnessing the power of this new generation of techniques, while also introducing the data analysis skills that these high-throughput techniques require. Written for the highly successful Methods in Molecular Biology series, 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.
Authoritative and up-to-date, Post-Transcriptional Gene Regulation, Third Edition serves as a versatile resource for researchers studying post-transcriptional regulation by both introducing the most recent techniques and providing a comprehensive guide to their implementation.
Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
List of contents
Introduction to Bioinformatics Resources for Post-Transcriptional Regulation of Gene Expression.- Predicting RNA Secondary Structure Using In Vitro and In Vivo Data.- RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment.- Analysis of mRNA Translation by Polysome Profiling.- Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling.- Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq.- Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation Systems.- Studying RNP Composition with RIP.- PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.- A Pipeline for Analyzing eCLIP and iCLIP Data with htseq-clip and DEWSeq.- Identification of miRNAs Bound to an RNA of Interest by MicroRNA Capture Affinity Technology (miR-CATCH).- Identifying the Protein Interactomes of Target RNAs Using HyPR-MS.- Visualization and Quantification of Subcellular RNA Localization Using Single Molecule RNA Fluorescence In Situ Hybridization.- Single-Molecule RNA Imaging Using Mango II Arrays.- Genome-Wide Identification of Polyadenylation Dynamics with TED-Seq.- In Vivo RNA Structure Probing with DMS-MaPseq.- Transcriptome-Wide Profiling of RNA Stability.- High-Throughput Quantitation of Yeast uORF Regulatory Impacts Using FACS-uORF.- m6A RNA Immunoprecipitation Followed by High-Throughput Sequencing to Map N6-Methyladenosine.- Detecting m6A with In Vitro DART-Seq.- Target-Specific Profiling of RNA m5C Methylation Level Using Amplicon Sequencing.- Transcriptome-Wide Identification of 2'-O-Methylation Sites with RibOxi-Seq.
