Preface ......................................................... v
Contributors ................................................... ix
1 Landscaping Plant Epigenetics ................................ 1
Peter C. McKeown and Charles Spillane
2 The Gene Balance Hypothesis: Dosage Effects in Plants ....... 25
James A. Bircbler and Reiner A. Veitia
3 High-Throughput RNA-Seq for Allelic or Locus-Specific
Expression Analysis in Arabidopsis-Related Species,
Hybrids, and Allotetraploids ................................ 33
Danny W-K. Ng, Xiaoli Shi, Gyoungju Nah, and Z. Jeffrey
Chen
4 Inference of Allele-Specific Expression from RNA-seq Data ... 49
Paul K. Korir and Cathal Seoighe
5 Screening for Imprinted Genes Using High-Resolution
Melting Analysis of PCR Amplicons ........................... 71
Robert Day and Richard Macknight
6 Analysis of Genomic Imprinting by Quantitative Allele-
Specific Expression by Pyrosequencing® ...................... 85
Peter C. McKeown, Antoine Fort, and Charles Spillane
7 Endosperm-Specific Chromatin Profiling by Fluorescence-
Activated Nuclei Sorting and Chip-on-Chip .................. 105
Isabelle Weinhofer and Claudia Köhler
8 Imaging Sexual Reproduction in Arabidopsis Using
Fluorescent Markers ........................................ 117
Mathieu Ingouff
9 Genome-Wide Analysis of DNA Methylation in Arabidopsis
Using MeDIP-Chip ........................................... 125
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 ............... 151
Emidio Albertini and Gianpiero Marconi
11 Detecting Histone Modifications in Plants .................. 165
Jie Song, Bas Rutjens, and Caroline Dean
12 Quantitatively Profiling Genome-Wide Patterns of Histone
Modifications in Arabidopsis thaliana Using ChlP-seq ....... 177
Chongyuan Luo and Eric Lam
13 Analysis of Retrotransposon Activity in Plants ............. 195
Christopher DeFraia and R. Keith Slotkin
14 Detecting Epigenetic Effects of Transposable Elements in
Plants ..................................................... 211
Christian Parisod, Armel Salmon, Malika Ainouche, and
Marie-Angele Grandbastien
15 Detection and Investigation of Transitive Gene Silencing
in Plants .................................................. 219
Leen Vermeersch, Nancy De Winne, and Ann Depicker
Index ......................................................... 243
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