Plant epigenetics : methods and protocols / edited by Igor Kovalchuk, Franz J. Zemp. — New York ; London : Springer, 2010. – (58.17/M592/v.631)

Contents

    Contents
    
    Preface
    Contributors
    1 Analysis of DNA Methylation in Plants by Bisulfite Sequencing
    2 Analysis of Bisulfite Sequencing Data from Plant DNA Using CyMATE
    3 Analysis of Locus-Specific Changes in Methylation Patterns Using a COBRA (Combined Bisulfite Restriction Analysis) Assay
    4 Detection of Changes in Global Genome Methylation Using the Cytosine-Extension Assay
    5 In Situ Analysis of DNA Methylation in Plants
    6 Analysis of Mutation/Rearrangement Frequencies and Methylation Patterns at a Given DNA Locus Using Restriction Fragment Length Polymorphism
    7 Isoschizomers and Amplified Fragment Length Polymorphism for the Detection of Specific Cytosine Methylation Changes
    8 Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays
    9 Northern Blotting Techniques for Small RNAs
    10 qRT-PCR of Small RNAs
    11 Cloning New Small RNA Sequences
    12 Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part A: ChIP-chip Molecular Methods
    13 Genome-Wide Mapping of Protein-DNA Interaction by Chromatin Immunoprecipitation and DNA Microarray Hybridization (ChIP-chip). Part B: ChIP-chip Data Analysis 161
    14 Metaanalysis of ChIP-chip Data 185
    15 Chromatin Immunoprecipitation Protocol for Histone Modifications and Protein-DNA Binding Analyses in Arabidopsis 209
    16 cDNA Libraries for Virus-Induced Gene Silencing 221
    17 Detection and Quantification of DNA Strand Breaks Using the ROPS (Random Oligonucleotide Primed Synthesis) Assay 237
    18 Reporter Gene-Based Recombination Lines for Studies of Genome Stability 243
    19 Plant Transgenesis
    Index