Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis -- Chromatin Conformation Capture-Based Analysis of Nuclear Architecture -- Metaanalysis of Genome-Wide Chromatin Data -- Localization of Mirnas by In Situ Hybridization in Plants using Conventional Oligonucleotide Probes -- COBRA (Combined Bisulfite Restriction Analysis) Assay for the Analysis of Locus-Specific Changes in Methylation Patterns -- Analysis of Global Genome Methylation Using the Cytosine-Extension Assay -- In Situ Analysis Of DNA Methylation In Plants -- Analysis of DNA Hydroxymethylation In Arabidopsis Using Colorimetric Assay -- Analysis of DNA Cytosine Methylation Patterns using Methylation Specific Amplification Polymorphism (MSAP) -- Differentially Methylated Region - Representational Difference Analysis (DMR-RDA): A Powerful Method to Identify Dmrs in Uncharacterized Genomes -- Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays -- Northern Blotting Techniques for Small RNAs -- Stem-Loop Qrt-PCR for the Detection of Plant Micrornas -- Profiling New Small RNA Sequences -- Small RNA Library Preparation and Illumina Sequencing in Plants -- Bioinformatics Analysis of Small RNA Transcriptomes - The Detailed Work Flow -- Increasing a Stable Transformation Efficiency of Arabidopsis by Manipulating the Endogenous Gene Expression using Virus-Induced Gene Silencing -- The Random Oligonucleotide-Primed Synthesis Assay for the Quantification of DNA Strand Breaks -- Profiling Transposable Elements and their Epigenetic Effects in Non-Model Species.

This volume provides a variety of protocols to analyze various epigenetic changes, including differential expression of non-coding RNAs, changes in DNA methylation, and histone modifications in plants. Chapters detail protocols with different degrees of complexity, and describe bioinformatics approaches for data processing and analysis. 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 Epigenetics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field. .