Plant Epigenetics: Methods and Protocols (Methods in Molecular Biology) Book

Preface v

Contributors ix

1 Analysis of DNA Methylation in Plants by Bisulfite Sequencing Andrea M. Foerster Ortrun Mittelsten Scheid 1

2 Analysis of Bisulfite Sequencing Data from Plant DNA Using CyMATE Andrea M. Foerster Jennifer Hetzl Christoph Müllner Ortrun Mittelsten Scheid 13

3 Analysis of Locus-Specific Changes in Methylation Patterns Using a COBRA (Combined Bisulfite Restriction Analysis) Assay Alex Boyko Igor Kovalchuk 23

4 Detection of Changes in Global Genome Methylation Using the Cytosine-Extension Assay Alex Boyko Igor Kovalchuk 33

5 In Situ Analysis of DNA Methylation in Plants Palak Kathiria Igor Kovalchuk 41

6 Analysis of Mutation/Rearrangement Frequencies and Methylation Patterns at a Given DNA Locus Using Restriction Fragment Length Polymorphism Alex Boyko Igor Kovalchuk 49

7 Isoschizomers and Amplified Fragment Length Polymorphism for the Detection of Specific Cytosine Methylation Changes Leonor Ruiz-García Jose Antonio Cabezas Nuria de María María-Teresa Cervera 63

8 Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays Martine Boccara Alexis Sarazin Bernard Billoud Agnes Bulski Louise Chapell David Baulcombe Vincent Colot 75

9 Northern Blotting Techniques for Small RNAs Todd Blevins 87

10 qRT-PCR of Small RNAs Erika Varkonyi-Gasic Roger P. Hellens 109

11 Cloning New Small RNA Sequences Yuko Tagami Naoko Inaba Yuichiro Watanabe 123

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 Franziska Turck 139

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 Julia Reimer Franziska Turck 161

14 Metaanalysis of ChIP-chip Data Julia Engelhorn Franziska Turck 185

15 Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis Stéphane Pien Ueli Grossniklaus 209

16 cDNA Libraries for Virus-Induced Gene Silencing Andrea T. Todd Enwu Liu Jonathan E. Page 221

17 Detection and Quantification of DNA Strand Breaks Using the ROPS (Random Oligonucleotide Primed Synthesis) Assay Alex Boyko Igor Kovalchuk 237

18 Reporter Gene-Based Recombination Lines for Studies of Genome Stability Palak Kathiria Igor Kovalchuk 243

19 Plant Transgenesis Alicja Ziemienowicz 253

Index 269