Plant Chromatin Dynamics: Methods and Protocols

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

B?n?dicte Desvoyes, Zaida Vergara, Joana Sequeira-Mendes, Sofia Madeira, and Crisanto Gutierrez

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

B?n?dicte 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 Fr?d?ric Pontvianne

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

Ana Karina Morao, Erwann Caillieux, Vincent Colot, and Fran?ois 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 Analysis

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

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 Garc?a-Aguilar and Daphn? Autran

24. Cell-type Specific Chromatin Analysis in Whole-mount Plant Tissues by Immunostaining

Wenjing She, C?lia Baroux, and Ueli Grossniklaus

25. Measuring Dynamic