Dassi Erik (ed.) Post-Transcriptional Gene Regulation

3rd edition. — Humana Press, 2022. — 412 p. — (Methods in Molecular Biology 2404). — ISBN 978-1-0716-1850-9.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.Bioinformatics
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
Expression Studies
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
Interactomics
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 Protein Interactomes of Target RNAs Using HyPR-MS
The RNA Lifecycle
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
RNA Modifications
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