Analysis of DNA Methylation in Plants by Bisulfite Sequencing -- Analysis of Bisulfite Sequencing Data from Plant DNA Using CyMATE -- Analysis of Locus-Specific Changes in Methylation Patterns Using a COBRA (Combined Bisulfite Restriction Analysis) Assay -- Detection of Changes in Global Genome Methylation Using the Cytosine-Extension Assay -- In Situ Analysis of DNA Methylation in Plants -- Analysis of Mutation/Rearrangement Frequencies and Methylation Patterns at a Given DNA Locus Using Restriction Fragment Length Polymorphism -- Isoschizomers and Amplified Fragment Length Polymorphism for the Detection of Specific Cytosine Methylation Changes -- Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays -- Northern Blotting Techniques for Small RNAs -- qRT-PCR of Small RNAs -- Cloning New Small RNA Sequences -- Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part A: ChIP-chip Molecular Methods -- Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data Analysis -- Metaanalysis of ChIP-chip Data -- Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis -- cDNA Libraries for Virus-Induced Gene Silencing -- Detection and Quantification of DNA Strand Breaks Using the ROPS (Random Oligonucleotide Primed Synthesis) Assay -- Reporter Gene-Based Recombination Lines for Studies of Genome Stability -- Plant Transgenesis.

The past fifteen years have witnessed major advances in epigenetics, one of the most popular and quickly evolving fields of modern science. In Plant Epigenetics: Methods and Protocols, expert researchers explore the most recent developments, examining in great detail the contribution of epigenetic regulation to cell function in plants. Chapters include a variety of protocols for studying the function of small non-coding RNAs, DNA methylation, and histone modifications in plants, often in different degrees of complexity. This volume describes bioinformatic approaches to the analysis of high-throughput data, such as bisulfite sequencing and Chip-on-chip assays. It features much-desired protocols for plant transgenesis and the analysis of genome stability, with a detailed discussion of their applications to epigenetic studies. Composed in the highly successful Methods in Molecular Biology™ series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Wide-ranging and innovative, Plant Epigenetics: Methods and Protocols is an invaluable manual designed to help researchers uncover the undiscovered and unexplained phenomena in plant biology.