The Integrated Stress Response: Methods and Protocols

ISBN-13: 9781071619773 / Angielski / Miękka / 2022 / 404 str.

Daniel Matějů; Jeffrey A. Chao

Opis

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.

Spis treści

Part I: Analysis of mRNA Translation Regulation

 

1. An Overview of Methods for Detecting eIF2α 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 Münch

 

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 Sidibé 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 Söhnel, 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 Padrón 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 Pérez-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, Jürgen Beneke, Holger Erfle, and Georg Stoecklin

 

23. APEX Proximity Labeling of Stress Granule Proteins

            Sara Elmsaouri, Sebastian Markmiller, and Gene W. Yeo