Chromatin Remodeling Factors and DNA Replication ................ 1
R. Varga-Weisz
1. Introduction ................................................ 1
2. Chromatin and Chromatin Remodeling Factors .................. 2
2.1. Chromatin ............................................. 2
2.2. Histone Modification Enzymes .......................... 3
2.3. ATP-Dependent Chromatin Remodeling Factors ............ 4
3. Chromatin Structure and DNA Replication ..................... 5
4. Chromatin Assembly .......................................... 7
4.1. Histone Chaperones .................................... 7
4.2. Chromatin Assembly Factor 1, a Replication-Coupled
Histone Chaperone ..................................... 9
4.3. CAF-1 Functions in the Inheritance of
Chromatin States ...................................... 9
4.4. Histone Chaperone ASF 1 .............................. 10
4.5. Histone Chaperones and Heterochromatin Replication ... 11
4.6. Histone Variants ..................................... 11
4.7. DNA Replication-Independent Chromatin Assembly ....... 12
5. Histone Modifications and Chromatin Replication ............ 13
5.1. Histone Deacetylation During Chromatin
Replication .......................................... 13
5.2. Histone Acetylation at the Replication Site .......... 13
6. ATP-Dependent Chromatin Remodeling Factors in
Chromatin Replication ...................................... 14
6.1. ISWI Complexes in Chromatin Assembly in Vitro ........ 14
6.2. ISWI Complexes and Their Role in Chromatin
Replication in Vivo .................................. 17
7. The Assembly of Higher Order Chromatin Structures .......... 19
8. PCNA, a Central Coordinator of Epigenetic Inheritance ...... 20
9. Mechanisms of Epigenetic Inheritance Through Chromatin:
Conclusion ................................................. 21
References ................................................. 21
Epigenetic Inheritance of Chromatin States Mediated by
Polycomb and Trithorax Group Proteins in Drosophila ............ 31
J. Déjardin and G. Cavalli
1. Introduction ............................................... 31
2. Proteins of the Polycomb Group of Genes .................... 33
2.1. PcG Complexes ........................................ 33
2.1.1. The ESC-E(Z) Complex ......................... 33
2.1.2. The Polycomb Repressive Complex 1 ............ 35
2.1.3. Other Identified PcG Proteins and Partners ... 36
2.2. Targeting of PcG-Mediated Repression ................. 37
2.2.1. PcG Response Elements ........................ 37
2.2.2. Chromatin Determinants Associated
with Targeting ............................... 39
2.3. Mechanisms of Repression ............................. 43
2.3.1. Spreading or Looping? ........................ 43
2.3.2. Proposed Silencing Mechanisms ................ 44
3. Proteins of the Trithorax Group ............................ 46
3.1. trxG Complexes ....................................... 48
3.1.1. The Trithorax Acetylation Complex (TACl) ..... 48
3.1.2. The Brahma Complex ........................... 48
3.1.3. The GAF-FACT Complex ......................... 49
3.1.4. Other trxG Complexes and Partners ............ 49
3.2. Targeting of trxG Complexes at TREs .................. 49
3.3. Mechanisms of Action ................................. 51
4. Modes of Inheritance ....................................... 54
5. Concluding Remarks ......................................... 55
References ................................................. 56
How to Pack the Genome for a Safe Trip ......................... 65
C. Caron, J. Govin, S. Rousseaux and S. Khochbin
1. Introduction ............................................... 65
2. Synthesis of Histone Variants .............................. 67
2.1. Non-Testis-Specific Core Histone Variants ............ 68
2.2. Testis-Specific Histone Variants ..................... 69
2.2.1. Linker Histones .............................. 69
2.2.2. Core Histones ................................ 70
3. Histone Modifications ...................................... 71
3.1. Acetylation .......................................... 72
3.2. Ubiquitination ....................................... 73
3.3. Phosphorylation ...................................... 73
3.4. Methylation .......................................... 74
4. Transition Proteins ........................................ 74
5. Final Components of the Sperm Chromatin .................... 75
5.1. Protamines ........................................... 76
5.2. Histones ............................................. 77
6. Mechanisms Controlling Post-Meiotic Chromatin
Reorganization: A General Discussion ....................... 77
6.1. Active Transcription Followed by Repression in
Round Spermatids ..................................... 78
6.2. Functional Link Between Histone Acetylation and
Chromatin Condensation and Histone Replacement ....... 79
6.3. Does Histone Ubiquitination Play a Role in
Spermatid-Specific Chromatin Remodeling? ............. 80
6.4. Is There a Spermiogenesis-Specific Histone Code? ..... 81
6.5. Do Histone Variants Play a Role in
Spermatid-Specific Chromatin Remodeling? ............. 82
7. Concluding Remarks ......................................... 82
References ................................................. 84
Chromatin Modifications on the Inactive X Chromosome ........... 91
H.R. Cohen, M.E. Royce-Tolland, K.A. Worringer and
B. Panning
1. Introduction ............................................... 91
2. Features of Xi Chromatin ................................... 92
2.1. Histone H3 Lysine 9 Methylation ...................... 92
2.2. Histone H3 Lysine 27 Methylation ..................... 94
2.3. Methylation at Other Histone H3 Residues ............. 95
2.4. Histone Acetylation .................................. 96
2.5. Histone MacroH2A ..................................... 97
2.6. Other Variant Histones ............................... 98
2.7. Nucleosome Position .................................. 98
2.8. Shape of the Xi ...................................... 98
2.9. DNA Methylation ...................................... 99
2.10. Late Replication Timing ............................. 100
2.11. XistRNA ............................................. 101
2.12. Redundant Mechanisms Maintain Silencing ............. 101
3. Chromatin at the Xic ...................................... 101
3.1. Histone Modifications ............................... 102
3.2. DNA Methylation ..................................... 102
3.3. Replication Timing .................................. 103
4. Genes that Escape X-Inactivation .......................... 103
4.1. Histone Modifications ............................... 103
4.2. DNA Methylation ..................................... 104
4.3. Replication Timing .................................. 104
4.4. Chromosome Organization ............................. 104
5. Developmental Regulation of X-Inactivation ................ 105
5.1. Three Stages of X-Inactivation ...................... 105
5.2. Embryonic Stem Cells ................................ 107
5.3. Extraembryonic Cells ................................ 108
5.4. Reactivation of the Xi .............................. 109
6. Chromatin Features of the X Chromosomes Prior to
X-Inactivation ............................................ 111
6.1. Imprinted X-Inactivation ............................ 111
6.2. Random X-Inactivation ............................... 112
7. Conclusion ................................................ 114
References ................................................ 115
Chromatin Mechanisms in Drosophila Dosage Compensation ........ 123
M. Taipale and A. Akhtar
1. Introduction .............................................. 123
2. The MSL Complex ........................................... 124
2.1. MSL-1 ............................................... 126
2.2. MSL-2 ............................................... 127
2.3. MSL-3 ............................................... 127
2.4. MOF ................................................. 128
2.5. MLE ................................................. 129
2.6. JIL-1 ............................................... 131
2.7. roXl and roX2 ....................................... 131
2.7.1. roX Genes as Non-Coding RNAs ................ 132
2.7.2. roX Loci as Chromatin Entry Sites ........... 132
3. Targeting, Assembly and Spreading of the MSL Complex ...... 133
3.1. Targeting and Assembly .............................. 133
3.2. Spreading ........................................... 135
4. Cracking the Code X ....................................... 136
4.1. Establishing the Code ............................... 136
4.2. Reading the Code .................................... 137
5. Molecular Mechanism of Dosage Compensation ................ 138
5.1. Initiation Versus Elongation ........................ 138
5.2. The Inverse Effect Hypothesis ....................... 139
6. The Origin and Evolution of the MSL Complex ............... 141
References ................................................ 143
DNA Methylation in Epigenetic Control of Gene Expression ...... 151
A. Razin and B. Kantor
1. Introduction .............................................. 151
2. Changes in Gene-Specific Methylation Patterns During
Early Embryo Development .................................. 153
3. Effect of Methylation on Gene Expression .................. 154
3.1. Direct Transcription Inhibition .................... 154
3.2. Indirect Transcription Inhibition ................... 156
4. DNA Methylation and Genomic Imprinting .................... 159
5. DNA Methylation and Disease ............................... 162
6. Concluding Remarks ........................................ 163
References ................................................ 163
The Epigenetic Breakdown of Cancer Cells: From
DNA Methylation to Histone Modifications ...................... 169
E. Ballestar and M. Esteller
1. Introduction .............................................. 169
2. What Is Responsible for DNA Methylation and for
How Deregulation Occurs? .................................. 171
3. Is Methylation Specific to the Tumor Type? ................ 173
4. Connecting DNA Methylation Changes with Transcription:
Chromatin Mechanisms ...................................... 174
5. Can We Reactivate Epigenetically Silenced Genes?
Towards Epigenetic Therapy ................................ 178
References ................................................ 178
Developmental Regulation of the β-Globin Gene Locus ........... 183
L. Chakalova, D. Carter, E. Debrand, B. Goyenechea,
A. Horton, J. Miles, C. Osborne and P. Fraser
1. Introduction .............................................. 183
2. The p-Globin Clusters and Their Ontogeny .................. 184
3. Models for Studying the β-Globin Locus .................... 185
4. The LCR Is Required for High-Level Expression ............. 186
5. The Role of Individual HS ................................. 188
6. Gene Competition and the LCR Holocomplex .................. 189
7. The β-Globin Locus Resides in a Region of
Tissue-Specific Open Chromatin ............................ 190
8. The Role of Insulators .................................... 191
9. Intergenic Transcription .................................. 192
10. Intergenic Promoters ...................................... 193
11. Histone Modification and Developmental
Globin Gene Expression .................................... 194
12. The Role of Intergenic Transcription ...................... 195
13. The Cell Cycle Connection ................................. 196
14. The Corfu Deletion ........................................ 197
15. Higher Order Folding and Long-Range Regulation ............ 198
16. Nuclear Organization ...................................... 199
17. Summary Model ............................................. 200
References ................................................ 201
Epigenetic Regulation of Mammalian Imprinted Genes:
From Primary to Functional Imprints ........................... 207
M. Weber, H. Hagège, N. Aptel, C. Brunel, G. Cathala
and T. Forné
1. Introduction .............................................. 207
2. Imprinting Evolution ...................................... 208
2.1. Conservation of Parental Genomic Imprinting
in Therian Mammals .................................. 208
2.2. Theories on the Evolution of Parental
Genomic Imprinting .................................. 209
2.2.1. The Parental Conflict Theory ................ 210
2.2.2. Alternative Theories ........................ 211
3. Characteristics of Mammalian Imprinted Genes .............. 211
4. Epigenetic Control of Imprinted Genes ..................... 212
4.1. DNA Methylation ..................................... 212
4.2. Histone Modifications ............................... 214
4.3. Asynchronous DNA Replication Timing ................. 215
4.4. Chromatin Architecture .............................. 216
5. The Parental Genomic Imprinting Cycle ..................... 216
5.1. Erasure ............................................. 216
5.2. Establishment ....................................... 218
5.2.1. Primary Imprinting Marks .................... 218
5.2.2. Imprinting Centres .......................... 219
5.3. Maintenance ......................................... 221
5.4. Monoallelic Expression of Imprinted Genes ........... 222
5.4.1. Formatting for Gene Expression .............. 223
5.4.2. Acquisition of Functional Imprints .......... 223
6. Conclusion ................................................ 225
References ................................................ 226
Seed Development and Genomic Imprinting in Plants ............. 237
C. Köhler and U. Grossniklaus
1. Introduction .............................................. 237
2. Seed Development in Angiosperms ........................... 238
3. Development and Function of the Endosperm ................. 238
4. A Role for Genomic Imprinting in Seed Development? ........ 241
5. The Discovery of Genomic Imprinting in Maize .............. 242
6. Studies on Other Potentially Imprinted Genes in Maize ..... 243
7. Maternal Control of Early Seed Development
in Arabidopsis ............................................ 244
8. Intragenomic Parental Conflict and the Evolution
of Genomic Imprinting ..................................... 246
9. Imprinting of the MEDEA Locus in Arabidopsis .............. 247
10. Function of MEDEA During Gametophyte and
Seed Development .......................................... 249
11. Imprinting of the FWA Locus in the Female Gametophyte ..... 251
12. The Role of Imprinting During Gametophyte and
Seed Development .......................................... 252
13. Imprinting and Apomixis ................................... 253
14. Possible Epigenetic Marks Distinguishing Maternal
and Paternal Alleles ...................................... 254
14.1. Chromatin Structure ................................. 254
14.2. DNA Methylation During Gametogenesis ................ 255
14.3. DNA Methylation During Seed Development ............. 256
15. Conclusions ............................................... 257
References ................................................ 257
Subject Index ................................................. 263
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