mRNA Decay

1. Front Matter

   Pages i-xi

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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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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.

• Decay pathways
• mRNA-binding protein targets
• Metabolic labeling
• RNAseq
• Bioinformatics
• Nonsense-mediated mRNA decay
• Tissue homeostasis regulation
• Genome-wide sequencing

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

  Shireen R. Lamandé

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