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(R) 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 Kohler 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, Rene Wardenaar, Maria Colome-Tatche, 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-Angele Grandbastien 15. Detection and Investigation of Transitive Gene Silencing Effects in Plants Leen Vermeersch, Nancy De Winne, and Ann Depicker