Post-transcriptional gene regulation
Author(s)
Bibliographic Information
Post-transcriptional gene regulation
（Methods in molecular biology / John M. Walker, series editor, 2404）（Springer protocols）
Humana Press, c2022 [i.e. 2021]
3rd ed
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Note
Previous ed.: 2016
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
Part I: Bioinformatics
1. Introduction to Bioinformatics Resources for Post-Transcriptional Regulation of Gene Expression
Eliana Destefanis and Erik Dassi
2. Predicting RNA Secondary Structure Using In Vitro and In Vivo Data
Riccardo Delli Ponti and Gian Gaetano Tartaglia
3. RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment
Inbal Paz, Amir Argoetti, Noa Cohen, Niv Even, and Yael Mandel-Gutfreund
Part II: Expression Studies
4. Analysis of mRNA Translation by Polysome Profiling
Anne Cammas, Pauline Herviou, Leila Dumas, and Stefania Millevoi
5. Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling
Alexander L. Cope, Sangeevan Vellappan, John S. Favate, Kyle S. Skalenko, Srujana S. Yadavalli, and Premal Shah
6. Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq
Sahil Sharma and Cynthia M. Sharma
7. Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation Systems
Katharina G. Wandera and Chase L. Beisel
Part III: Interactomics
8. Studying RNP Composition with RIP
Annalisa Rossi and Alberto Inga
9. PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites
Charles Danan, Sudhir Manickavel, and Markus Hafner
10. A Pipeline for Analyzing eCLIP and iCLIP Data with htseq-clip and DEWSeq
Sudeep Sahadevan, Thileepan Sekaran, and Thomas Schwarz
11. Identification of miRNAs Bound to an RNA of Interest by MicroRNA Capture Affinity Technology (miR-CATCH)
Andrea Zeni, Margherita Grasso, and Michela A. Denti
12. Identifying the Protein Interactomes of Target RNAs Using HyPR-MS
Katherine B. Henke, Rachel M. Miller, Rachel A. Knoener, Mark Scalf, Michele Spiniello, and Lloyd M. Smith
Part IV: The RNA Lifecycle
13. Visualization and Quantification of Subcellular RNA Localization Using Single Molecule RNA Fluorescence In Situ Hybridization
Ankita Arora, Raeann Goering, Pedro Tirado Velez, and J. Matthew Taliaferro
14. Single-Molecule RNA Imaging Using Mango II Arrays
Adam D. Cawte, Haruki Iino, Peter J. Unrau, and David S. Rueda
15. Genome-Wide Identification of Polyadenylation Dynamics with TED-Seq
Yeonui Kwak and Hojoong Kwak
16. In Vivo RNA Structure Probing with DMS-MaPseq
Paromita Gupta and Silvia Rouskin
17. Transcriptome-Wide Profiling of RNA Stability
Nina Fasching, Jan Petrzilek, Niko Popitsch, Veronika Herzog, and Stefan L. Ameres
18. High-Throughput Quantitation of Yeast uORF Regulatory Impacts Using FACS-uORF
Gemma E. May and C. Joel McManus
Part V: RNA Modifications
19. m6A RNA Immunoprecipitation Followed by High-Throughput Sequencing to Map N6-Methyladenosine
Devi Prasad Bhattarai and Francesca Aguilo
20. Detecting m6A with In Vitro DART-Seq
Matthew Tegowski1, Huanyu Zhu, and Kate D. Meyer
21. Target-Specific Profiling of RNA m5C Methylation Level Using Amplicon Sequencing
Tennille Sibbritt, Ulrike Schumann, Andrew Shafik, Marco Guarnacci, Susan J. Clark, and Thomas Preiss
22. Transcriptome-Wide Identification of 2'-O-Methylation Sites with RibOxi-Seq
Yinzhou Zhu, Christopher L. Holley, and Gordon G. Carmichael
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