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Alternative Splicing

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Peter Scheiffele

    1. Biozentrum, University of Basel, Basel, Switzerland

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  2. Oriane Mauger

    1. Biozentrum, University of Basel, Basel, Switzerland

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2537)

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About this book

This detailed volume collects commonly used and cutting-edge methods to analyze alternative splicing, a key step in gene regulation. After an introduction of the alternative splicing mechanism and its targeting for therapeutic strategies, the book continues with techniques for analyzing alternative splicing profiles in complex biological systems, visualizing and localizing alternative spliced transcripts with cellular and sub-cellular resolution, probing regulators of alternative splicing, as well as assessing the functional consequences of alternative splicing. Written for the highly successful Methods in Molecular Biology series, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Alternative Splicing: Methods and Protocols serves as an ideal guide for both RNA aficionados that want to implement novel approaches in their labs and novices undertaking alternative splicing projects.

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Keywords

Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Alternative Splicing in Human Biology and Disease

    • Daniel Jutzi, Marc-David Ruepp
    Pages 1-19

  3. Targeting Alternative Splicing for Therapeutic Interventions

    • Jessica L. Centa, Michelle L. Hastings
    Pages 21-36

  4. An Optimized Protocol for the Mapping of Cell Type–Specific Ribosome-Associated Transcript Isoforms from Small Mouse Brain Regions

    • Giulia Di Bartolomei, Peter Scheiffele
    Pages 37-49

  5. FACS-Based Neuronal Cell Type–Specific RNA Isolation and Alternative Splicing Analysis

    • Zicheng Wei, Yuxin Qin, Gordon Fishell, Boxing Li
    Pages 51-62

  6. Quantitative Measurement of Alternatively Spliced RNA Isoform Levels

    • Zhelin Jeff Li, Sika Zheng
    Pages 63-79

  7. Analysis of Splicing Regulation by Third-Generation Sequencing

    • Eric Allemand, Fabrice Ango
    Pages 81-95

  8. Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework

    • André Gohr, Federica Mantica, Antonio Hermoso-Pulido, Javier Tapial, Yamile Márquez, Manuel Irimia
    Pages 97-128

  9. Identification and Quantification of Microexons Using Bulk and Single-Cell RNA-Seq Data

    • Guillermo E. Parada, Martin Hemberg
    Pages 129-147

  10. Functional Annotation of Custom Transcriptomes

    • Fursham Hamid, Kaur Alasoo, Jaak Vilo, Eugene Makeyev
    Pages 149-172

  11. Design, Labeling, and Application of Probes for RNA smFISH

    • Ewa Piskadlo, Bastian Th. Eichenberger, Luca Giorgetti, Jeffrey A. Chao
    Pages 173-183

  12. BaseScope™ Approach to Visualize Alternative Splice Variants in Tissue

    • Alexandra Bunda, Arturo Andrade
    Pages 185-196

  13. In Situ Imaging of mRNA Splicing Variants by SpliceRCA

    • Xiaojun Ren, Jinghong Li
    Pages 197-209

  14. Two-Color Fluorescent Reporters for Analysis of Alternative Splicing

    • John A. Calarco, Pallavi P. Pilaka-Akella
    Pages 211-229

  15. Quantitative Detection of Protein Splice Variants by Selected Reaction Monitoring (SRM) Mass Spectrometry

    • Alexander Schmidt, Dietmar Schreiner
    Pages 231-246

  16. Probing the Interactions of Splicing Regulatory Small Molecules and Proteins with U1 snRNP Using NMR Spectroscopy

    • Sébastien Campagne, Tebbe de Vries, Frédéric H. -T. Allain
    Pages 247-262

  17. Genome-Wide CRISPR Screening to Identify Mammalian Factors that Regulate Intron Retention

    • Anna M. Scarborough, Ashwin Govindan, Nicholas K. Conrad
    Pages 263-284

  18. Tethered Function Assays to Elucidate the Role of RNA-Binding Proteins

    • Andrea B. Eberle, Oliver Mühlemann
    Pages 285-306

  19. Probing Liquid–Liquid Phase Separation of RNA-Binding Proteins In Vitro and In Vivo

    • Stephanie Heinrich, Maria Hondele
    Pages 307-333

  20. Analysis of Oligonucleotide Biodistribution and Metabolization in Experimental Animals

    • François Halloy, Paulina Brönnimann, Jonathan Hall, Daniel Schümperli
    Pages 335-350
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Editors and Affiliations

  • Biozentrum, University of Basel, Basel, Switzerland

    Peter Scheiffele, Oriane Mauger

Bibliographic Information

  • Book Title: Alternative Splicing

  • Book Subtitle: Methods and Protocols

  • Editors: Peter Scheiffele, Oriane Mauger

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2521-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2520-0Published: 28 July 2022

  • Softcover ISBN: 978-1-0716-2523-1Published: 28 July 2023

  • eBook ISBN: 978-1-0716-2521-7Published: 27 July 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 354

  • Number of Illustrations: 4 b/w illustrations, 57 illustrations in colour

  • Topics: Genetics and Genomics

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