Nucleosomes, Histones and Chromatin Part B

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