Plant Epigenetics: Methods and Protocols

1. Chromatin ImmunoprecipitationProtocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis

Wanhui You, Stéphane Pien, and UeliGrossniklaus

2.Chromatin Conformation Capture-Based Analysis of Nuclear Architecture

3.Metaanalysis of Genome-Wide Chromatin Data

4.Localization of Mirnas by In Situ Hybridization in Plants using ConventionalOligonucleotide Probes

5.COBRA (Combined Bisulfite Restriction Analysis) Assay for the Analysis ofLocus-Specific Changes in Methylation Patterns

6.Analysis of Global Genome Methylation Using the Cytosine-Extension Assay

AndriyBilichak and Igor Kovalchuk

7.In Situ Analysis Of DNA Methylation in Plants

PalakKathiria and Igor Kovalchuk

8. Analysis of DNA Hydroxymethylation in Arabidopsis UsingColorimetric Assay

Andrey Golubov and Igor Kovalchuk

9. Analysis of DNA Cytosine Methylation Patterns usingMethylation Specific Amplification Polymorphism (MSAP)

María Ángeles Guevara, Nuria De María, Enrique Sáez-Laguna,María Dolores Vélez, María Teresa Cervera, and José Antonio Cabezas

10. Differentially MethylatedRegion - Representational Difference Analysis (DMR-RDA): A Powerful Method to IdentifyDmrs in Uncharacterized Genomes

11. Analysis of Small RNA Populations UsingHybridization to DNA Tiling Arrays

MartineBoccara, Alexis Sarazin, Bernard Billoud, Agnes Bulski, Louise Chapell, DavidBaulcombe, and Vincent Colot

12. Northern Blotting Techniques for Small RNAs

ToddBlevins

13. Stem-Loop QRT-PCR for the Detection of PlantMicrornas

Erika Varkonyi-Gasic

14.Profiling New Small RNA Sequences

Masayuki Tsuzuki and Yuichiro Watanabe

15.Small RNA Library Preparation and Illumina Sequencing in Plants

AndriyBilichak, Andrey Golubov, and Igor Kovalchuk

16.Bioinformatics Analysis of Small RNA Transcriptomes - The Detailed Work Flow<

SlavaIlnytskyy and Andriy Bilichak

17. Increasinga Stable Transformation Efficiency of Arabidopsis by Manipulating theEndogenous Gene Expression using Virus-Induced Gene Silencing

18.The Random Oligonucleotide-Primed Synthesis Assay for the Quantification of DNAStrand Breaks

AndriyBilichak and Igor Kovalchuk

19.Profiling Transposable Elements and their Epigenetic Effects in Non-ModelSpecies

ChristianParisod