Plant Epigenetics

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.

Table of contents

Preface
Contributors
1. Analysis of DNA Methylation in Plants by Bisulfite Sequencing
Andrea M. Foerster and Ortrun Mittelsten Scheid
2. Analysis of bisulfite sequencing data from plant DNA with CyMATE
Andrea M. Foerster, Jennifer Hetzl, Christoph Müllner and Ortrun Mittelsten Scheid
3. Analysis of locus-specific changes in methylation patterns using a COBRA (combined bisulfite restriction analysis) assay
Alex Boyko and Igor Kovalchuk
4. Detection of changes in global genome methylation using the cytosine-extension assay
Alex Boyko and Igor Kovalchuk
5. In situ analysis of DNA methylation in plants
Palak Kathiria and Igor Kovalchuk
6. Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using RFLP (restriction fragment length polymorphism)
Alex Boyko and Igor Kovalchuk
7. 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
8. 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
9. Northern blotting techniques for small RNAs
Todd Blevins
10. qRT-PCR of small RNAs
Erika Varkonyi-Gasic and Roger P. Hellens
11. Cloning new small RNA sequences
Yuko Tagami, Naoko Inaba and Yuichiro Watanabe
12. Genome-wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part A – ChIP-chip Molecular Methods
Julia J. Reimer and Franziska Turck
13. 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
14. Metaanalysis of ChIP-chip data
Julia Engelhorn and Franziska Turck
15. Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis
Stéphane Pien, Ueli Grossniklaus
16. cDNA Libraries for Virus-Induced Gene Silencing
Andrea T. Todd, Enwu Liu and Jonathan E. Page
17. Detection and quantification of DNA strand breaks using the ROPS (random oligonucleotide primed synthesis) assay
Alex Boyko and Igor Kovalchuk
18. Reporter gene-based recombination lines for studies of genome stability
Palak Kathiria and Igor Kovalchuk
19. Plant transgenesis
Alicja Ziemienowicz