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The discovery of DNA as the genetic material brought great hope to scientists all over the world. It was believed that many of the lingering questions in genetics and the mechanisms of heredity would fnally be answered. However, as often is the case in science, more qu- tions arose out of this discovery. What defnes a gene? What are the mechanisms of gene regulation? Further discovery and technological innovations brought about sequencing techniques that allowed the study of complete genomes from many organisms, including Arabidopsis and humans. Despite all the excitement surrounding these technologies, many features of the genome remained unclear. Peculiar characteristics in genome composition such as signifcant redundancy consisting of many repetitive elements and noncoding sequences, active transcriptional units with no protein product, and unusual sequences in promoter regions added to the mysteries of genetic make-up and gene regulation. Indeed, the more we discovered about the genome, the more diffcult it became to understand the complexity of cellular function and regulation. Out of the study of the intricacies of the genome and gene regulation, arose a new science that was independent of actual DNA changes, but critical in maintaining gene regulation and genetic stability. Epigenetics, literally translated as "above genetics," is the science that describes the mechanisms of heritable changes in gene regulation that does not involve modifcations of DNA sequence. These changes may last through somatic cell division and, in some cases, throughout multiple generations.
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Table of Contents

Table of Contents Preface Contributors Analysis of DNA Methylation in Plants by Bisulfite Sequencing Andrea M. Foerster and Ortrun Mittelsten Scheid Analysis of bisulfite sequencing data from plant DNA with CyMATE Andrea M. Foerster, Jennifer Hetzl, Christoph Mullner and Ortrun Mittelsten Scheid Analysis of locus-specific changes in methylation patterns using a COBRA (combined bisulfite restriction analysis) assay Alex Boyko and Igor Kovalchuk Detection of changes in global genome methylation using the cytosine-extension assay Alex Boyko and Igor Kovalchuk In situ analysis of DNA methylation in plants Palak Kathiria and Igor Kovalchuk Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using RFLP (restriction fragment length polymorphism) Alex Boyko and Igor Kovalchuk Isoschizomers and Amplified Fragment Length Polymorphism (AFLP) for the Detection of Specific Cytosine Methylation Changes Leonor Ruiz-Garcia, Jose Antonio Cabezas, Nuria de Maria, Maria-Teresa Cervera Analysis of small RNA populations using hybridization to DNA tiling arrays Martine Boccara, Alexis Sarazin, Bernard Billoud, Agnes Bulski, Louise Chapell, David Baulcombe and Vincent Colot Northern blotting techniques for small RNAs Todd Blevins qRT-PCR of small RNAs Erika Varkonyi-Gasic and Roger P. Hellens Cloning new small RNA sequences Yuko Tagami, Naoko Inaba and Yuichiro Watanabe Genome-wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNAMicroarray Hybridization (ChIP-chip). Part A - ChIP-chip Molecular Methods Julia J. Reimer and Franziska Turck Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part B - ChIP-chip data analysis Ulrike Gobel and Franziska Turck Metaanalysis of ChIP-chip data Julia Engelhorn and Franziska Turck Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis Stephane Pien, Ueli Grossniklaus cDNA Libraries for Virus-Induced Gene Silencing Andrea T. Todd, Enwu Liu and Jonathan E. Page Detection and quantification of DNA strand breaks using the ROPS (random oligonucleotide primed synthesis) assay Alex Boyko and Igor Kovalchuk Reporter gene-based recombination lines for studies of genome stability Palak Kathiria and Igor Kovalchuk Plant transgenesis Alicja Ziemienowicz

Reviews

From the reviews:"The book by Kovalchuk and Zemp is a successful attempt to provide the most recent approaches for identifying epigenetic variation in plants. ... it is without doubts that the publication should be in every bookcase of molecular scientists interested in epigenetics. I can also recommend it for plant ecologists and evolutionists engaged in epigenetic variation in plants because some methods can be a good improvement of the currently commonly used approaches." (Vit Latzel, Folia Geobotanica, Vol. 48, 2013)

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