Plant chromatin dynamics : methods and protocols
著者
書誌事項
Plant chromatin dynamics : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, v. 1675）（Springer protocols）
Humana Press : Springer Science+Business Media, c2018
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注記
"This Humana Press imprint is published by Springer Nature"--Title page verso
Includes bibliographical references and index
内容説明・目次
内容説明
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.
目次
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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