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mRNA Processing

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Yongsheng Shi

    1. Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, USA

    View editor publications

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  • Includes cutting-edge methods and protocols for the study of mRNA processing
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1648)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Detection and Identification of Uncapped RNA by Ligation-Mediated Reverse Transcription Polymerase Chain Reaction

    • C. Kiong Ho
    Pages 1-9

  3. Preparation of Splicing Competent Nuclear Extract from Mammalian Cells and In Vitro Pre-mRNA Splicing Assay

    • Maliheh Movassat, Hossein Shenasa, Klemens J. Hertel
    Pages 11-26

  4. Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS)

    • Joerg E. Braun, Victor Serebrov
    Pages 27-37

  5. In Vitro Modulation of Endogenous Alternative Splicing Using Splice-Switching Antisense Oligonucleotides

    • Jeong Eun Park, Luca Cartegni
    Pages 39-52

  6. Purification of mRNA Processing Complexes Using an RNA Affinity Approach

    • Xiuye Wang, Yongsheng Shi
    Pages 53-63

  7. Polyadenylation Site-Based Analysis of Transcript Expression by 3′READS+

    • Dinghai Zheng, Bin Tian
    Pages 65-77

  8. Comprehensive Identification of mRNA Polyadenylation Sites by PAPERCLIP

    • Hun-Way Hwang, Robert B. Darnell
    Pages 79-93

  9. Microinjection and Fluorescence In Situ Hybridization Assay for Studying mRNA Export in Mammalian Cells

    • Ke Wang, Min Shi, Hong Cheng
    Pages 95-102

  10. Methods for the Detection of Adenosine-to-Inosine Editing Events in Cellular RNA

    • Eimile Oakes, Pranathi Vadlamani, Heather A. Hundley
    Pages 103-127

  11. Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants

    • Shayna Stein, Emad Bahrami-Samani, Yi Xing
    Pages 129-142

  12. Inducible Expression of Eukaryotic Circular RNAs from Plasmids

    • Deirdre C. Tatomer, Dongming Liang, Jeremy E. Wilusz
    Pages 143-154

  13. Methods for Extraction of RNA, Proteins, or Protein Complexes from Subcellular Compartments of Eukaryotic Cells

    • Kyu-Hyeon Yeom, Andrey Damianov
    Pages 155-167

  14. Isolation of Newly Transcribed RNA Using the Metabolic Label 4-Thiouridine

    • Angela Garibaldi, Francisco Carranza, Klemens J. Hertel
    Pages 169-176

  15. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP)

    • Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt et al.
    Pages 177-200Open Access

  16. Purification of Transcript-Specific mRNP Complexes Formed In Vivo from Saccharomyces cerevisiae

    • Jenna E. Smith, Kristian E. Baker
    Pages 201-220

  17. A Cell-Based High-Throughput Method for Identifying Modulators of Alternative Splicing

    • Sika Zheng
    Pages 221-233

  18. Genome-Wide RNAi Screens for RNA Processing Events in Drosophila melanogaster S2 Cells

    • Natoya Peart, Eric J. Wagner
    Pages 235-245

  19. Assaying RNA Structure Inside Living Cells with SHAPE

    • Chao Feng, Dalen Chan, Robert C. Spitale
    Pages 247-256

  20. Erratum to: Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP)

    • Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt et al.
    Pages E1-E1
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Keywords

About this book

This detailed volume assembles a number of the most commonly used and state-of-the-art methodologies in the revolutionary field of mRNA processing in order to aid researchers in choosing the best method for their specific problems. Given that the vast majority of alternative mRNA processing events has yet to be explored, these techniques promise to breathe new life into the myriad new ideas currently underway. 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. 

Practical and easy to use, mRNA Processing: Methods and Protocols seeks to aid scientists venturing into what’s certain to be another explosive period of growth in this dynamic field of study.


The chapter 'Robust, Cost-EffectiveProfiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP)' is published open access under a CC BY 4.0 license at link.springer.com. 

Editors and Affiliations

  • Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, USA

    Yongsheng Shi

Bibliographic Information

  • Book Title: mRNA Processing

  • Book Subtitle: Methods and Protocols

  • Editors: Yongsheng Shi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7204-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-7203-6Published: 02 August 2017

  • Softcover ISBN: 978-1-4939-8415-2Published: 12 August 2018

  • eBook ISBN: 978-1-4939-7204-3Published: 01 August 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 258

  • Number of Illustrations: 16 b/w illustrations, 33 illustrations in colour

  • Topics: Human Genetics

  • Industry Sectors: Biotechnology, Pharma

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