Description

This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. The volume covers nucleosomes, histones and chromatin and has chapters on dynamic mapping of histone-DNA interactions in nucleosomes by unzipping single molecules of DNA, digital DNase technology, and genome-wide analysis of chromatin transition.

Key Features

  • Contains quality chapters authored by leaders in the field
  • The volume covers nucleosomes, histones and chromatin
  • Has chapters on dynamic mapping of histone-DNA interactions in nucleosomes by unzipping single molecules of DNA, digital DNase technology, and genome-wide analysis of chromatin transition

Readership

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists

Table of Contents

Series Page

Contributors

Preface

Volume in series

Chapter One DNA Translocation of ATP-Dependent Chromatin Remodeling Factors Revealed by High-Resolution Optical Tweezers

1 Introduction

2 Instrument

3 Remodeler Translocation on Bare DNA

4 Nucleosome-Dependent Remodeler Translocation

5 Data Analysis

Chapter Two Unzipping Single DNA Molecules to Study Nucleosome Structure and Dynamics

1 Introduction

2 Sample Preparation

3 Instrumentation and Data Collection

4 Data Processing

5 Determination of Unzipping Accuracy and Precision

6 Unzipping in Nucleosome Studies

7 Conclusions

Chapter Three Monitoring Conformational Dynamics with Single-Molecule Fluorescence Energy Transfer: Applications in Nucleosome Remodeling

1 Introduction

2 Preparation of Fluorescently Labeled Sample for Single-Molecule FRET Imaging

3 Preparing PEG-Coated Slides with Sample Chamber

4 Optical Setup and Single-Molecule FRET Data Acquisition

5 Data Analysis

6 Summary

Chapter Four 4C Technology: Protocols and Data Analysis

1 Introduction

2 4C Template Preparation

3 4C-Seq Primer Design and PCR

4 High-Throughput Sequencing of 4C PCR Products

5 Data Analysis

Chapter Five A Torrent of Data: Mapping Chromatin Organization Using 5C and High-Throughput Sequencing

1 Introduction

2 Preparing Torrent 5C Libraries

3 Overview of the Ion Torrent Sequencing Protocol

4 Torrent 5C Data Processing

5 Conclusion

Chapter Six Genome-Wide Mapping of Nucleosomes in Yeast Using Paired-End Sequencing

1 Introduction

2 Preparation of Nucleosome Core Particles from Yeast

3 Preparation of Core Particle DNA for Sequencing

4 Paired-End Sequencing

5 Bioinformatic Analysis of Nucleosome Sequences

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Details

No. of pages:
408
Language:
English
Copyright:
© 2012
Published:
Imprint:
Academic Press
Electronic ISBN:
9780123919397
Print ISBN:
9780123919380

About the serial-volume-editors