Front Matter ....Pages i-xiv
Front Matter ....Pages 1-1
Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming (Clara Bourbousse, Moussa Benhamed, Fredy Barneche)....Pages 3-30
Profiling DNA Methylation Using Bisulfite Sequencing (BS-Seq) (Yun-Ru Chen, Sheng Yu, Silin Zhong)....Pages 31-43
Bisulfite Sequencing Using Small DNA Amounts (Susanne Edelmann, Stefan Scholten)....Pages 45-60
Identification of Differentially Methylated Regions in the Genome of Arabidopsis thaliana (Kamal Kishore, Mattia Pelizzola)....Pages 61-69
A Rapid and Efficient ChIP Protocol to Profile Chromatin Binding Proteins and Epigenetic Modifications in Arabidopsis (Bénédicte Desvoyes, Zaida Vergara, Joana Sequeira-Mendes, Sofia Madeira, Crisanto Gutierrez)....Pages 71-82
Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP) (Bénédicte Desvoyes, Joana Sequeira-Mendes, Zaida Vergara, Sofia Madeira, Crisanto Gutierrez)....Pages 83-97
A Method to Identify Nucleolus-Associated Chromatin Domains (NADs) (Marie-Christine Carpentier, Ariadna Picart-Picolo, Frédéric Pontvianne)....Pages 99-109
Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins (Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier)....Pages 111-130
Mapping of Histone Modifications in Plants by Tandem Mass Spectrometry (Walid Mahrez, Lars Hennig)....Pages 131-145
Histone H1 Purification and Post-Translational Modification Profiling by High–Resolution Mass Spectrometry (Maciej Kotliński, Andrzej Jerzmanowski)....Pages 147-166
Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis (Alice Pajoro, Jose M. Muiño, Gerco C. Angenent, Kerstin Kaufmann)....Pages 167-181
Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq (Marko Bajic, Kelsey A. Maher, Roger B. Deal)....Pages 183-201
Front Matter ....Pages 203-203
Unraveling the Complex Epigenetic Mechanisms that Regulate Gene Activity (Marian Bemer)....Pages 205-231
Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture (Stefan Grob, Giacomo Cavalli)....Pages 233-246
3C in Maize and Arabidopsis (Blaise Weber, Suraj Jamge, Maike Stam)....Pages 247-270
Profiling Histone Modifications in Synchronized Floral Tissues for Quantitative Resolution of Chromatin and Transcriptome Dynamics (Julia Engelhorn, Frank Wellmer, Cristel C. Carles)....Pages 271-296
De Novo Identification of sRNA Loci and Non-coding RNAs by High-Throughput Sequencing (Alice Lunardon, Cristian Forestan, Silvia Farinati, Serena Varotto)....Pages 297-314
Identification of In Planta Protein–Protein Interactions Using IP-MS (Suraj Jamge, Gerco C. Angenent, Marian Bemer)....Pages 315-329
RNA Immunoprecipitation Protocol to Identify Protein–RNA Interactions in Arabidopsis thaliana (Benoit Mermaz, Fuquan Liu, Jie Song)....Pages 331-343
In Vitro Assays to Measure Histone Methyltransferase Activity Using Different Chromatin Substrates (Yannick Jacob, Philipp Voigt)....Pages 345-360
Identification of Parent-of-Origin-Dependent QTLs Using Bulk-Segregant Sequencing (Bulk-Seq) (Nuno D. Pires, Ueli Grossniklaus)....Pages 361-371
QTLepi Mapping in Arabidopsis thaliana (Kathrin Lauss, Joost J. B. Keurentjes)....Pages 373-394
Front Matter ....Pages 395-395
A Compendium of Methods to Analyze the Spatial Organization of Plant Chromatin (Aline V. Probst)....Pages 397-418
Localization of Chromatin Marks in Arabidopsis Early Embryos (Marcelina García-Aguilar, Daphné Autran)....Pages 419-441
Cell-Type Specific Chromatin Analysis in Whole-Mount Plant Tissues by Immunostaining (Wenjing She, Célia Baroux, Ueli Grossniklaus)....Pages 443-454
Measuring Dynamics of Histone Proteins by Photobleaching in Arabidopsis Roots (Stefanie Rosa)....Pages 455-465
Fluorescence In Situ Hybridization (FISH) and Immunolabeling on 3D Preserved Nuclei (Till David Bey, Maria Koini, Paul Fransz)....Pages 467-480
High-Affinity LNA–DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana (Lauriane Simon, Aline V. Probst)....Pages 481-491
A Method for Testing Random Spatial Models on Nuclear Object Distributions (Javier Arpòn, Valérie Gaudin, Philippe Andrey)....Pages 493-507
Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes (Václaclav Bačovský, Roman Hobza, Boris Vyskot)....Pages 509-535
Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations (Célia Baroux, Veit Schubert)....Pages 537-589
Automated 3D Gene Position Analysis Using a Customized Imaris Plugin: XTFISHInsideNucleus (Mariamawit S. Ashenafi, Célia Baroux)....Pages 591-613
Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ (Sophie Desset, Axel Poulet, Christophe Tatout)....Pages 615-632
Transmission Electron Microscopy Imaging to Analyze Chromatin Density Distribution at the Nanoscale Level (Tohnyui Ndinyanka Fabrice, Lusik Cherkezyan, Christoph Ringli, Célia Baroux)....Pages 633-651
Back Matter ....Pages 653-659