Plant Epigenetics

The past fifteen years have witnessed major advances in epigenetics, one of the most popular and quickly evolving fields of modern science. In Plant Epigenetics: Methods and Protocols, expert researchers explore the most recent developments, examining in great detail the contribution of epigenetic regulation to cell function in plants. Chapters include a variety of protocols for studying the function of small non-coding RNAs, DNA methylation, and histone modifications in plants, often in different degrees of complexity. This volume describes bionformatic approaches to the analysis of highthroughput data, such as bisulfite sequencing and Chip-on-chip assays. It features much-desired protocols for plant transgenesis and the analysis of genome stability, with a detailed discussion of their applications to epigenetic studies. Composed in the highly successful Methods in Molecular Biology'„¢ series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls.Wide-ranging and innovative, Plant Epigenetics: Methods and Protocols is an invaluable manual designed to help researchers uncover the undiscovered and unexplained phenomena in plant biology.

Preface	p. v
Contributors	p. ix
Analysis of DNA Methylation in Plants by Bisulfite Sequencing	p. 1
Analysis of Bisulfite Sequencing Data from Plant DNA Using CyMATE	p. 13
Analysis of Locus-Specific Changes in Methylation Patterns Using a COBRA (Combined Bisulfite Restriction Analysis) Assay	p. 23
Detection of Changes in Global Genome Methylation Using the Cytosine-Extension Assay	p. 33
In Situ Analysis of DNA Methylation in Plants	p. 41
Analysis of Mutation/Rearrangement Frequencies and Methylation Patterns at a Given DNA Locus Using Restriction Fragment Length Polymorphism	p. 49
Isoschizomers and Amplified Fragment Length Polymorphism for the Detection of Specific Cytosine Methylation Changes	p. 63
Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays	p. 75
Northern Blotting Techniques for Small RNAs	p. 87
qRT-PCR of Small RNAs	p. 109
Cloning New Small RNA Sequences	p. 123
Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part A: ChIP-chip Molecular Methods	p. 139
Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data Analysis	p. 161
Metaanalysis of ChIP-chip Data	p. 185
Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis	p. 209
cDNA Libraries for Virus-Induced Gene Silencing	p. 221
Detection and Quantification of DNA Strand Breaks Using the ROPS (Random Oligonucleotide Primed Synthesis) Assay	p. 237
Reporter Gene-Based Recombination Lines for Studies of Genome Stability	p. 243
Plant Transgenesis	p. 253
Index	p. 269
Table of Contents provided by Ingram. All Rights Reserved.

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