Plant Chromatin Dynamics, 1st ed. 2018 Methods and Protocols Methods in Molecular Biology Series, Vol. 1675

This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into three sections detail the profiling of chromatin features in relation to epigenetic regulation, investigate the interaction between chromatin modifications and gene regulation, and explore the 3D spatial organization of the chromatin inside the nucleus. 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.

1. Section Overview: Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming

Clara Bourbousse, Moussa Benhamed, and Fredy Barneche

2. Profiling DNA Methylation using Bisulfite Sequencing (BS-Seq)

3. Bisulfite Sequencing using Small DNA Amounts

Susanne Edelmann and Stefan Scholten

4. Identification of Differentially Methylated Regions in the Genome of Arabidopsis thaliana

Kamal Kishore and Mattia Pelizzola

5. A Rapid and Efficient ChIP Protocol to Profile Chromatin Binding Proteins and Epigenetic Modifications in Arabidopsis

6. Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP)

Bénédicte Desvoyes, Joana Sequeira-Mendes, Zaida Vergara, Sofia Madeira, and Crisanto Gutierrez

7. A Method to Identify Nucleolus-Associated Chromatin Domains (NADs)

Marie-Christine Carpentier, Ariadna Picart-Picolo, and Frédéric Pontvianne

8. Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins

Ana Karina Morao, Erwann Caillieux, Vincent Colot, and François Roudier

9. Mapping of Histone Modifications in Plants by Tandem Mass Spectrometry

10. Histone H1 Purification and Post-Translational Modification Profiling by High–Resolution Mass Spectrometry

Maciej Kotliński and Andrzej Jerzmanowski

Alice Pajoro, Jose M. Muiňo, Gerco Angenent, and Kerstin Kaufmann

11. Identification of Open Chromatin Regions in Plant Genomes using ATAC-Seq

Marko Bajic, Kelsey A. Maher, and Roger B. Deal

Part I: Chromatin Dynamics and Gene Regulation

12. Section Overview: Unravelling the Complex Epigenetic Mechanisms that Regulate Gene Activity

Marian Bemer

13. Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture

14. 3C in Maize and Arabidopsis

15. Profiling Histone Modifications in Synchronised Floral Tissues for Quantitative Resolution of Chromatin and Transcriptome Dynamics

Julia Engelhorn, Frank Wellmer, and Cristel C. Carles

16. De Novo Identification of sRNA Loci and Non-Coding RNAs by High-Throughput Sequencing

Alice Lunardon, Christian Forestan, Silvia Farinati, and Serena Varotto

17. Identification of in planta Protein-Protein Interactions using IP-MS

Suraj Jamge, Gerco C. Angenent, and Marian Bemer

18. RNA Immunoprecipitation Protocol to Identify Protein-RNA Interactions in Arabidopsis thaliana

Benoit Mermaz, Fuquan Liu, and Jie Song

19. In vitro Assays to Measure Histone Methyltransferase Activity using Different Chromatin Substrates

Yannick Jacob and Philipp Voigt

20. Identification of Parent-of-Origin-Dependent QTLs using Bulk-Segregant Sequencing (Bulk-Seq)

Nuno D. Pires and Ueli Grossniklaus

21. QTL^epi mapping in Arabidopsis thaliana

Kathrin Lauss and Joost J.B. Keurentjes

PART II: Spatial Chromatin Organization

22. Section Overview: a Compendium of Methods to Analyze the Spatial Organization of Plant Chromatin

Aline Probst

23. Localisation of Chromatin Marks in Arabidopsis Early Embryos

Marcelina García-Aguilar and Daphné Autran

Wenjing She, Célia Baroux, and Ueli Grossniklaus

25. Measuring Dynamics of Histone Proteins by Photobleaching in Arabidopsis Roots

Stefanie Rosa

26. Fluorescence In Situ Hybridization (FISH) and Immunolabeling on 3D Preserved Nuclei

Till David Bey, Maria Koini, and Paul Fransz

27. High-Affinity LNA/DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana

28. A Method for Testing Random Spatial Model on Nuclear Object Distributions

Javier Arpòn, Valérie Gaudin, and Philippe Andrey

Václav Bačovský, Roman Hobza, and Boris Vyskot

30. Technical Review: Microscopy and Image Processing Tools to Analyse Plant Chromatin – Practical Considerations

Célia Baroux and Veit Schubert

31. Automated 3D Gene Position Analysis using a Customized Imaris Plugin: XTFISHInsideNucleus

Mariamawit S. Ashenafi and Célia Baroux

32. Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole Mount Plant Tissue using NucleusJ

33. Transmission Electron Microscopy Imaging to Analyse Chromatin Density Distribution at the Nanoscale Level

Tohnyui Ndinyanka Fabrice, Lusik Cherkezyan, Christoph Ringli, and Célia Baroux 

Includes cutting-edge methods protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras