Plant Epigenetics and Epigenomics: Methods and Protocols

1. Landscaping Plant Epigenetics

Peter C. McKeown and Charles Spillane

2. The Gene Balance Hypothesis: Dosage Effects in Plants

James A. Birchler and Reiner A. Veitia

3. High-throughput RNA-Seq for Allelic or Locus-specific Expression Analysis in Arabidopsis Related Species, Hybrids, and Allotetraploids

Danny W-K. Ng, Xiaoli Shi, Gyoungju Nah, and Z. Jeffrey Chen

4. Inference of Allele-specific Expression from RNA-seq Data

Paul K. Korir and Cathal Seoighe

5. Screening for Imprinted Genes using High Resolution Melting Analysis of PCR Amplicons

Robert Day and Richard Macknight

6. Analysis of Genomic Imprinting by Quantitative Allele-specific Expression by Pyrosequencing®

Peter C. McKeown, Antoine Fort, and Charles Spillane

7. Endosperm-specific Chromatin Profiling by Fluorescence-activated Nuclei Sorting and Chip-on-chip

Isabelle Weinhofer and Claudia Köhler

8. Imaging Sexual Reproduction in Arabidopsis using Fluorescent Markers

Mathieu Ingouff

9. Genome-wide Analysis of DNA Methylation in Arabidopsis using MeDIP-chip

Sandra Cortijo, René Wardenaar, Maria Colomé-Tatché, Frank Johannes, and Vincent Colot

10. Methylation-Sensitive Amplified Polymorphism (MSAP) Marker to Investigate Drought-stress Response in Montepulciano and Sangiovese Grape Cultivars

Emidio Albertini and Gianpiero Marconi

11. Detecting Histone Modifications in Plants

Jie Song, Bas Rutjens, and Caroline Dean

12. Quantitatively Profiling Genome-wide Patterns of Histone Modifications in Arabidopsis thaliana using ChIP-seq

Chongyuan Luo and Eric Lam

13. Analysis of Retrotransposon Activity in Plants

Christopher DeFraia and R. Keith Slotkin

14. Detecting Epigenetic Effects of Transposable Elements in Plants

Christian Parisod, Armel Salmon, Malika Ainouche, and Marie-Angèle Grandbastien

15. Detection and Investigation of Transitive Gene Silencing Effects in Plants

Leen Vermeersch, Nancy De Winne, and Ann Depicker