Main description:

This volume provides an up-to-date collection of protocols describing some of the key methods to investigate the integrated stress response (ISR), a vital evolutionarily conserved mechanism that enables eukaryotic cells to adapt to stress conditions and alter their gene expression programs. The content of the book is split between techniques to analyze mRNA translation regulation and methods to analyze interaction networks and ribonucleoprotein (RNP) granules. 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 practical, The Integrated Stress Response: Methods and Protocols serves as an ideal guide to help accelerate research into the complex and fascinating biology of the ISR.

Contents:

Part I: Analysis of mRNA Translation Regulation

1. An Overview of Methods for Detecting eIF2 Phosphorylation and the Integrated Stress Response

Agnieszka Krzyzosiak, Aleksandra Pitera, and Anne Bertolotti

2. CRISPR-Based Screening for Stress Response Factors in Mammalian Cells

Xiaoyan Guo and Martin Kampmann

3. Multiplexed Analysis of Human uORF Regulatory Functions during the ISR Using PoLib-Seq

Gemma E. May and C. Joel McManus

4. Measuring Bulk Translation Activity in Single Mammalian Cells during the Integrated Stress Response

Alyssa M. English and Stephanie L. Moon

5. Quantitative Translation Proteomics Using mePROD

Kevin Klann and Christian Munch

6. Quantifying the Binding of Fluorescently Labelled Guanine Nucleotides and Initiator tRNA to Eukaryotic Translation Initiation Factor 2

Martin D. Jennings and Graham D. Pavitt

7. Mammalian In Vitro Translation Systems

Yulia Gonskikh, Valentina Pecoraro, and Norbert Polacek

8. Measuring Repeat-Associated Non-AUG (RAN) Translation

Shaopeng Wang and Shuying Sun

9. Analysis of Ribosome Profiling Data

Carine Legrand, Khanh Dao Duc, and Francesca Tuorto

10. Analysis of Translational Control in the Integrated Stress Response by Polysome Profiling

Michael J. Holmes, Jagannath Misra, and Ronald C. Wek

11. High-Resolution Ribosome Profiling for Determining Ribosome Functional States during Translation Elongation

Mohammad Shafieinouri, Britnie Santiago Membreno, and Colin Chih-Chien Wu

12. Fluorescence Intensity-Based eIF2B's Guanine Nucleotide-Exchange Factor Activity Assay

Yusuke Sekine, David Ron, and Alisa F. Zyryanova

Part II: Analysis of Interaction Networks and RNP Granules

13. Collective Learnings of Studies of Stress Granule Assembly and Composition

Hadjara Sidibe and Christine Vande Velde

14. Detecting Stress Granules in Drosophila Neurons

Fabienne De Graeve, Nadia Formicola, Kavya Vinayan Pushpalatha, Akira Nakamura, Eric Debreuve, Xavier Descombes, and Florence Besse

15. Monitoring and Quantification of the Dynamics of Stress Granule Components in Living Cells by Fluorescence Decay after Photoactivation

Anna-Carina Soehnel, Nataliya I. Trushina, and Roland Brandt

16. Probing Protein Solubility Patterns with Proteomics for Insight into Network Dynamics

Xiaojing Sui, Mona Radwan, Dezerae Cox, and Danny M. Hatters

17. Analyzing the Composition and Organization of Ribonucleoprotein Complexes by APEX-Seq

Alejandro Padron and Nicholas Ingolia

18. Differential Analysis of the Nuclear and the Cytoplasmic RNA Interactomes in Living Cells

Michael Backlund and Andreas E. Kulozik

19. Identification of RNA-RBP Interactions in Subcellular Compartments by CLIP-Seq

Sonu Sahadevan, Manuela Perez-Berlanga, and Magdalini Polymenidou

20. Monitoring Virus-Induced Stress Granule Dynamics Using Long-Term Live-Cell Imaging

Vera Magg, Philipp Klein, and Alessia Ruggieri

21. Single-Molecule Imaging of mRNA Interactions with Stress Granules

Tatsuya Morisaki and Timothy J. Stasevich

22. Image-Based Screening for Stress Granule Regulators

Katharina Hoerth, Nina Eiermann, Jurgen Beneke, Holger Erfle, and Georg Stoecklin

23. APEX Proximity Labeling of Stress Granule Proteins

Sara Elmsaouri, Sebastian Markmiller, and Gene W. Yeo