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mRNA Decay

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Shireen R. Lamandé

    1. Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Australia

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  • Includes cutting-edge methods and protocols for the study of mRNA decay
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1720)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. 5′-Bromouridine IP Chase (BRIC)-Seq to Determine RNA Half-Lives

    • Toshimichi Yamada, Naoto Imamachi, Rena Onoguchi-Mizutani, Katsutoshi Imamura, Yutaka Suzuki, Nobuyoshi Akimitsu
    Pages 1-13

  3. Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq)

    • Farah Abdul-Rahman, David Gresham
    Pages 15-24

  4. Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcription and Decay

    • Wei Sun, Wei Chen
    Pages 25-34

  5. Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH

    • Tatjana Trcek, Samir Rahman, Daniel Zenklusen
    Pages 35-54

  6. PAR-CLIP for Discovering Target Sites of RNA-Binding Proteins

    • Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, Thomas Tuschl
    Pages 55-75

  7. Characterizing mRNA Sequence Motifs in the 3′-UTR Using GFP Reporter Constructs

    • Rene Geissler, Andrew Grimson
    Pages 77-88

  8. iCLIP of the PIWI Protein Aubergine in Drosophila Embryos

    • Bridlin Barckmann, Jérémy Dufourt, Martine Simonelig
    Pages 89-110

  9. Integration of ENCODE RNAseq and eCLIP Data Sets

    • Jorge Boucas
    Pages 111-129

  10. Identifying miRNA Targets Using AGO-RIPseq

    • Rebecca Petri, Johan Jakobsson
    Pages 131-140

  11. Integrated Analysis of miRNA and mRNA Expression Profiles to Identify miRNA Targets

    • Zhiming Li, Chi-Meng Tzeng
    Pages 141-148

  12. Identifying RISC Components Using Ago2 Immunoprecipitation and Mass Spectrometry

    • Tingfang Yi
    Pages 149-159

  13. Using Tet-Off Cells and RNAi Knockdown to Assay mRNA Decay

    • Thomas D. Baird, J. Robert Hogg
    Pages 161-173

  14. Identifying Cellular Nonsense-Mediated mRNA Decay (NMD) Targets: Immunoprecipitation of Phosphorylated UPF1 Followed by RNA Sequencing (p-UPF1 RIP−Seq)

    • Tatsuaki Kurosaki, Mainul Hoque, Lynne E. Maquat
    Pages 175-186

  15. Generation of Cell Lines Stably Expressing a Fluorescent Reporter of Nonsense-Mediated mRNA Decay Activity

    • Nadezhda M. Markina, Anton P. Pereverzev, Dmitry B. Staroverov, Konstantin A. Lukyanov, Nadya G. Gurskaya
    Pages 187-204

  16. Reactivation Assay to Identify Direct Targets of the Nonsense-Mediated mRNA Decay Pathway in Drosophila

    • Jonathan O. Nelson, Mark M. Metzstein
    Pages 205-211

  17. Studying Nonsense-Mediated mRNA Decay in Mammalian Cells Using a Multicolored Bioluminescence-Based Reporter System

    • Andrew Nickless, Zhongsheng You
    Pages 213-224

  18. Back Matter

    Pages 225-227
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Keywords

About this book

This detailed volume explores the latest methods that can be used to probe mRNA decay pathways and identify mRNA-binding protein targets as well as miRNA targets. Subjects include metabolic labelling and RNAseq methods for determining RNA decay rates, approaches for discovering RNA-binding protein targets, bioinformatics, miRNA targets and novel components of the miRNA-directed decay pathway, and recently developed approaches for studying nonsense-mediated mRNA decay, among other areas. Written for the highly popular 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 practical, mRNA Decay: Methods and Protocols serves as an ideal guide for molecular biologists, geneticists, and developmental biologists with an interest in understanding how normal development and tissue homeostasis is regulated and how these processes are perturbed in inherited and acquired diseases.

Editors and Affiliations

  • Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Australia

    Shireen R. Lamandé

Bibliographic Information

  • Book Title: mRNA Decay

  • Book Subtitle: Methods and Protocols

  • Editors: Shireen R. Lamandé

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7540-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7539-6Published: 15 December 2017

  • Softcover ISBN: 978-1-4939-8515-9Published: 30 August 2018

  • eBook ISBN: 978-1-4939-7540-2Published: 13 December 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 227

  • Number of Illustrations: 10 b/w illustrations, 24 illustrations in colour

  • Topics: Human Genetics

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