Section Overview: Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming -- Profiling DNA Methylation using Bisulfite Sequencing (BS-Seq) -- Bisulfite Sequencing using Small DNA Amounts -- Identification of Differentially Methylated Regions in the Genome of Arabidopsis thaliana -- A Rapid and Efficient ChIP Protocol to Profile Chromatin Binding Proteins and Epigenetic Modifications in Arabidopsis -- Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP) -- A Method to Identify Nucleolus-Associated Chromatin Domains (NADs) -- Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins -- Mapping of Histone Modifications in Plants by Tandem Mass Spectrometry -- Histone H1 Purification and Post-Translational Modification Profiling by High-Resolution Mass Spectrometry -- Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis -- Identification of Open Chromatin Regions in Plant Genomes using ATAC-Seq -- Section Overview: Unravelling the Complex Epigenetic Mechanisms that Regulate Gene Activity -- Technical Review: A Hitchhiker's Guide to Chromosome Conformation Capture -- 3C in Maize and Arabidopsis -- Profiling Histone Modifications in Synchronised Floral Tissues for Quantitative Resolution of Chromatin and Transcriptome Dynamics -- De Novo Identification of sRNA Loci and Non-Coding RNAs by High-Throughput Sequencing -- Identification of in planta Protein-Protein Interactions using IP-MS -- RNA Immunoprecipitation Protocol to Identify Protein-RNA Interactions in Arabidopsis thaliana -- In vitro Assays to Measure Histone Methyltransferase Activity using Different Chromatin Substrates -- Identification of Parent-of-Origin-Dependent QTLs using Bulk-Segregant Sequencing (Bulk-Seq) -- QTLepi mapping in Arabidopsis thaliana -- Section Overview: a Compendium of Methods to Analyze the Spatial Organization of Plant Chromatin -- Localisation of Chromatin Marks in Arabidopsis Early Embryos -- Cell-type Specific Chromatin Analysis in Whole-mount Plant Tissues by Immunostaining -- Measuring Dynamics of Histone Proteins by Photobleaching in Arabidopsis Roots -- Fluorescence In Situ Hybridization (FISH) and Immunolabeling on 3D Preserved Nuclei -- High-Affinity LNA/DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana -- A Method for Testing Random Spatial Model on Nuclear Object Distributions -- Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes -- Technical Review: Microscopy and Image Processing Tools to Analyse Plant Chromatin - practical Considerations -- Automated 3D Gene Position Analysis using a Customized Imaris Plugin: XTFISHInsideNucleus -- Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole Mount Plant Tissue using NucleusJ -- Transmission Electron Microscopy Imaging to Analyse Chromatin Density Distribution at the Nanoscale Level. .

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.