Plant Chromatin Dynamics

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 usingATAC-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 EarlyEmbryos.- 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.