Plant Epigenetics: Methods and Protocols

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 Müllner 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-García, Jose Antonio Cabezas, Nuria de María, María-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 Göbel 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 Stéphane 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