Nucleosomes, Histones and Chromatin Part B - 1st Edition - ISBN: 9780123919380, 9780123919397

Nucleosomes, Histones and Chromatin Part B, Volume 513

1st Edition

Serial Volume Editors: Carl Wu C. Allis
eBook ISBN: 9780123919397
Hardcover ISBN: 9780123919380
Imprint: Academic Press
Published Date: 10th September 2012
Page Count: 408
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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

6 Some General Experimental Considerations

Chapter Seven Measuring Genome-Wide Nucleosome Turnover Using CATCH-IT

1 Introduction

2 Covalent Attachment of Tagged Histones to Capture and Identify Turnover

3 Modified Solexa Library Preparation

Chapter Eight DNA Methyltransferase Accessibility Protocol for Individual Templates by Deep Sequencing

1 Introduction

2 Materials

3 Protocols

Chapter Nine Genome-Wide In Vitro Reconstitution of Yeast Chromatin with In Vivo-Like Nucleosome Positioning

1 Introduction

2 Preparation of Yeast WCE

3 Preparation of Histones

4 Expansion of Genomic Plasmid Library

5 Chromatin Reconstitution by Salt Gradient Dialysis

6 Incubation of Salt Gradient Dialysis Chromatin with WCE or Purified Factors

7 Generation of Mononucleosomes by Limited MNase Digestion

8 Summary

Chapter Ten Genome-Wide Mapping of Nucleosome Positions in Yeast Using High-Resolution MNase ChIP-Seq

1 Introduction

2 Methodology

Chapter Eleven Preparation of Drosophila Tissue Culture Cells from Different Stages of the Cell Cycle for Chromatin Immunoprecipitation Using Centrifugal Counterflow Elutriation and Fluorescence-Activated Cell Sorting

1 Introduction

2 Centrifugal Elutriation of Drosophila Cells to Obtain G1, S, and G2 Populations

3 FACS Sorting of Drosophila Cells to Obtain Mitotic Cell Populations

4 Summary

Chapter Twelve Genome-Wide Polyadenylation Site Mapping

1 Introduction

2 General Recommendations

3 Sample Preparation

4 Library Construction

5 Bioinformatic Analysis of Polyadenylation Site Sequencing Reads

6 Quality Control

7 Preparation of Double-Stranded Linkers

8 Summary

Chapter Thirteen Genome-Wide Mapping of Nucleosome Occupancy, Histone Modifications, and Gene Expression Using Next-Generation Sequencing Technology

1 Introduction

2 Mapping Genome-Wide Nucleosome Occupancy and Positions by High-Throughput Next-Generation Sequencing

3 Mapping Histone Modifications Using ChIP-Seq

4 Mapping Genome-Wide mRNA Profiles Using RNA-Seq

5 RNA-Seq Analysis with a Small Number of Cells

Chapter Fourteen A Chemical Approach to Mapping Nucleosomes at Base Pair Resolution in Yeast

1 Introduction

2 Construction of H4S47C S. cerevisiae Strain

3 Chemical Cleavage of Nucleosome Center Positions

4 Statistical Analysis of Chemical Mapping Data

5 Summary

Author Index

Subject Index


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


Details

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

About the Serial Volume Editors

Carl Wu Serial Volume Editor

Affiliations and Expertise

National Cancer Institute, Bethesda, MD

C. Allis Serial Volume Editor

Affiliations and Expertise

The Rockefeller University, New York, NY