Plant Epigenetics (2^nd Ed., Softcover reprint of the original 2nd ed. 2017)
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1456

This volume provides a variety of protocols to analyze various epigenetic changes, including differential expression of non-coding RNAs, changes in DNA methylation, and histone modifications in plants. Chapters detail protocols with different degrees of complexity, and describe bioinformatics approaches for data processing and analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Plant Epigenetics: Methods and Protocols, Second Editionaims to ensure successful results in the further study of this vital field.

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

Wanhui You, Stéphane Pien, and Ueli Grossniklaus

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 Conventional Oligonucleotide Probes

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

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

Andriy Bilichak and Igor Kovalchuk

7. In Situ Analysis Of DNA Methylation in Plants

Palak Kathiria and Igor Kovalchuk

8. Analysis of DNA Hydroxymethylation in Arabidopsis Using Colorimetric Assay

Andrey Golubov and Igor Kovalchuk

9. Analysis of DNA Cytosine Methylation Patterns using Methylation 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 Methylated Region - Representational Difference Analysis (DMR-RDA): A Powerful Method to Identify Dmrs in Uncharacterized Genomes

11. 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

12. Northern Blotting Techniques for Small RNAs

Todd Blevins

13. Stem-Loop QRT-PCR for the Detection of Plant Micrornas

Erika Varkonyi-Gasic

14. Profiling New Small RNA Sequences

Masayuki Tsuzuki and Yuichiro Watanabe

15. Small RNA Library Preparation and Illumina Sequencing in Plants

Andriy Bilichak, Andrey Golubov, and Igor Kovalchuk

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

Slava Ilnytskyy and Andriy Bilichak

17. Increasing a Stable Transformation Efficiency of Arabidopsis by Manipulating the Endogenous Gene Expression using Virus-Induced Gene Silencing

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

Andriy Bilichak and Igor Kovalchuk

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

Christian Parisod

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts