Chromatin remodeling : methods and protocols / edited by Randall H. Morse. — New York : Humana Press, c2012. – (58.17/M592/v.833)

Contents

    Contents
    
    Preface
    Contributors
    1 Strain Construction and Screening Methods for a Yeast Histone H3/H4 Mutant Library
    2 Measuring Dynamic Changes in Histone Modifications and Nucleosome Density during Activated Transcription in Budding Yeast
    3 Monitoring the Effects of Chromatin Remodelers on Long-Range Interactions In Vivo
    4 Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease
    5 Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay
    6 Assaying Chromatin Structure and Remodeling by Restriction Enzyme Accessibility
    7 Generation of DNA Circles in Yeast by Inducible Site-Specific Recombination
    8 An Efficient Purification System for Native Minichromosome from Saccharomyces cerevisiae
    9 Simultaneous Single-Molecule Detection of Endogenous C-5 DNA Methylation and Chromatin Accessibility Using MAPit
    10 Analysis of Stable and Transient Protein-Protein Interactions
    11 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence Recovery After Photobleaching 153
    12 Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence Correlation Spectroscopy and Temporal Image Correlation Spectroscopy 177
    13 Analysis of Chromatin Structure in Plant Cells
    14 Analysis of Histones and Histone Variants in Plants
    15 Reconstitution of Modified Chromatin Templates for In Vitro Functional Assays
    16 A Defined In Vitro System to Study ATP-Dependent Remodeling of Short Chromatin Fibers 255
    17 In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning on Yeast DNA
    18 Activator-Dependent Acetylation of Chromatin Model Systems
    19 Mapping Assembly Favored and Remodeled Nucleosome Positions on Polynucleosomal Templates
    20 Analysis of Changes in Nucleosome Contbrmation Using Fluorescence Resonance Energy Transfer
    21 Preparation of Nucleosomes Containing a Specific H2A-H2A Cross-Link Forming a DNA-Constraining Loop Structure
    22 Sulfyhydryl-Reactive Site-Directed Cross-Linking as a Method for Probing the Tetrameric Structure of Histones H3 and H4 373
    23 Genomic Approaches for Determining Nucleosome Occupancy in Yeast
    24 Genome-Wide Approaches to Determining Nucleosome Occupancy in Metazoans Using MNase-Seq
    25 Salt Fractionation of Nucleosomes for Genome-Wide Profiling
    26 Quantitative Analysis of Genome-Wide Chromatin Remodeling
    27 Computational Analysis of Nucleosome Positioning
    Index