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
Bénédicte Desvoyes, Zaida Vergara, Joana Sequeira-Mendes, Sofia Madeira, and Crisanto Gutierrez
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
Walid Mahrez and Lars Hennig
10. Histone H1 Purification and Post-Translational Modification Profiling by High-Resolution Mass Spectrometry
Maciej Kotliński and Andrzej Jerzmanowski
10. Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational AnalysisAlice 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
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 García-Aguilar and Daphné Autran
24. Cell-type Specific Chromatin Analysis in Whole-mount Plant Tissues by ImmunostainingWenjing She, Célia Baroux, and Ueli Grossniklaus
25. Measuring Dynamic
