Epigenetics and Chromatin (eBook)

Preface 6
Contents 8
Chromatin Remodeling Factors and DNA Replication 15
1 Introduction 15
2 Chromatin and Chromatin Remodeling Factors 16
3 Chromatin Structure and DNA Replication 19
4 Chromatin Assembly 21
5 Histone Modifications and Chromatin Replication 27
6 ATP-Dependent Chromatin Remodeling Factors in Chromatin Replication 28
7 The Assembly of Higher Order Chromatin Structures 33
8 PCNA, a Central Coordinator of Epigenetic Inheritance 34
9 Mechanisms of Epigenetic Inheritance Through Chromatin: Conclusion 35
References 35
Epigenetic Inheritance of Chromatin States Mediated by Polycomb and Trithorax Group Proteins in Drosophila 45
1 Introduction 45
2 Proteins of the Polycomb Group of Genes 47
3 Proteins of the Trithorax Group 60
4 Modes of Inheritance 68
5 Concluding Remarks 69
References 70
How to Pack the Genome for a Safe Trip 78
1 Introduction 78
2 Synthesis of Histone Variants 80
3 Histone Modifications 84
4 Transition Proteins 87
5 Final Components of the Sperm Chromatin 88
6 Mechanisms Controlling Post-Meiotic Chromatin Reorganization: A General Discussion 90
7 Concluding Remarks 95
References 97
Chromatin Modifications on the Inactive X Chromosome 103
1 Introduction 103
2 Features of Xi Chromatin 104
3 Chromatin at the Xic 113
4 Genes that Escape X-Inactivation 115
5 Developmental Regulation of X-Inactivation 117
6 Chromatin Features of the X Chromosomes Prior to X- Inactivation 123
7 Conclusion 126
References 127
Chromatin Mechanisms in Drosophila Dosage Compensation 135
1 Introduction 135
2 The MSL Complex 136
3 Targeting, Assembly and Spreading of the MSL Complex 145
4 Cracking the Code X 148
5 Molecular Mechanism of Dosage Compensation 150
6 The Origin and Evolution of the MSL Complex 153
References 155
DNA Methylation in Epigenetic Control of Gene Expression 162
1 Introduction 162
2 Changes in Gene-Specific Methylation Patterns During Early Embryo Development 164
3 Effect of Methylation on Gene Expression 165
4 DNA Methylation and Genomic Imprinting 170
5 DNA Methylation and Disease 173
6 Concluding Remarks 174
References 174
The Epigenetic Breakdown of Cancer Cells: From DNA Methylation to Histone Modifications 179
1 Introduction 179
2 What Is Responsible for DNA Methylation and for How Deregulation Occurs? 181
3 Is Methylation Specific to the Tumor Type? 183
4 Connecting DNA Methylation Changes with Transcription: Chromatin Mechanisms 184
5 Can We Reactivate Epigenetically Silenced Genes? Towards Epigenetic Therapy 188
References 188
Developmental Regulationof the b-Globin Gene Locus 192
1 Introduction 192
2 The b-Globin Clusters and Their Ontogeny 193
3 Models for Studying the b-Globin Locus 194
4 The LCR Is Required for High-Level Expression 195
5 The Role of Individual HS 197
6 Gene Competition and the LCR Holocomplex 198
7 The b-Globin Locus Resides in a Regionof Tissue-Specific Open Chromatin 199
8 The Role of Insulators 200
9 Intergenic Transcription 201
10 Intergenic Promoters 202
11 Histone Modification and Developmental Globin Gene Expression 203
12 The Role of Intergenic Transcription 204
13 The Cell Cycle Connection 205
14 The Corfu Deletion 206
15 Higher Order Folding and Long-Range Regulation 207
16 Nuclear Organization 208
17 Summary Model 209
References 210
Epigenetic Regulation of Mammalian Imprinted Genes: From Primary to Functional Imprints 216
1 Introduction 216
2 Imprinting Evolution 217
3 Characteristics of Mammalian Imprinted Genes 220
4 Epigenetic Control of Imprinted Genes 221
5 The Parental Genomic Imprinting Cycle 225
6 Conclusion 234
References 235
Seed Development and Genomic Imprinting in Plants 246
1 Introduction 246
2 Seed Development in Angiosperms 247
3 Development and Function of the Endosperm 249
4 A Role for Genomic Imprinting in Seed Development? 250
5 The Discovery of Genomic Imprinting in Maize 251
6 Studies on Other Potentially Imprinted Genes in Maize 252
7 Maternal Control of Early Seed Development in Arabidopsis 253
8 Intragenomic Parental Conflict and the Evolution of Genomic Imprinting 255
9 Imprinting of the MEDEA Locus in Arabidopsis 256
10 Function of MEDEA During Gametophyte and Seed Development 258
11 Imprinting of the FWA Locus in the Female Gametophyte 260
12 The Role of Imprinting During Gametophyte and Seed Development 261
13 Imprinting and Apomixis 262
14 Possible Epigenetic Marks Distinguishing Maternal and Paternal Alleles 263
15 Conclusions 266
References 266
Subject Index 272