CiNii Books - Plant chromatin dynamics : methods and protocols

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. Authoritative and cutting-edge, Plant Chromatin Dynamics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Table of Contents

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) Yun-Ru Chen, Sheng Yu, and Silin Zhong 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 Benedicte Desvoyes, Zaida Vergara, Joana Sequeira-Mendes, Sofia Madeira, and Crisanto Gutierrez 6. Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP) Benedicte 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 Frederic Pontvianne 8. Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins Ana Karina Morao, Erwann Caillieux, Vincent Colot, and Francois Roudier 9. Mapping of Histone Modifications in Plants by Tandem Mass Spectrometry Walid Mahrez and Lars Hennig 10. Histone H1 Purification and Post-Translational Modification Profiling by High-Resolution Mass Spectrometry Maciej Kotlinski and Andrzej Jerzmanowski 10. Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis Alice Pajoro, Jose M. Muino, 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 Stefan Grob and Giacomo Cavalli 14. 3C in Maize and Arabidopsis Blaise Weber, Suraj Jamge, and Maike Stam 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. QTLepi 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 Garcia-Aguilar and Daphne Autran 24. Cell-type Specific Chromatin Analysis in Whole-mount Plant Tissues by Immunostaining Wenjing She, Celia 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 Lauriane Simon and Aline V. Probst 28. A Method for Testing Random Spatial Model on Nuclear Object Distributions Javier Arpon, Valerie Gaudin, and Philippe Andrey 29. Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes Vaclav Bacovsky, Roman Hobza, and Boris Vyskot 30. Technical Review: Microscopy and Image Processing Tools to Analyse Plant Chromatin - Practical Considerations Celia Baroux and Veit Schubert 31. Automated 3D Gene Position Analysis using a Customized Imaris Plugin: XTFISHInsideNucleus Mariamawit S. Ashenafi and Celia Baroux 32. Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole Mount Plant Tissue using NucleusJ Sophie Desset, Axel Poulet, and Christophe Tatout 33. Transmission Electron Microscopy Imaging to Analyse Chromatin Density Distribution at the Nanoscale Level Tohnyui Ndinyanka Fabrice, Lusik Cherkezyan, Christoph Ringli, and Celia Baroux

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Plant chromatin dynamics : methods and protocols

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