| List of Contributors xi |
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| Bases of Chromatin Signaling and Their Impact on Diseases Pathogenesis xiii |
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| I Histone Mark Writers |
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1 Histone Acetyltransferases, Key Writers of the Epigenetic Language |
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3 | (22) |
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3 | (1) |
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Functional and Mechanistic Impact of Histone Acetylation |
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4 | (1) |
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Identification of the First Histone Acetyltransferases, a Historical Perspective |
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5 | (3) |
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Yeast Histone Acetyltransferases Belong to Three Different Families |
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8 | (3) |
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Three Families of Metazoan Histone Acetyltransferases and Their Roles in Animal Development |
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11 | (4) |
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Role of Histone Acetyltransferases in the Pathogenesis of Human Diseases |
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15 | (2) |
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Conclusions and Future Directions |
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17 | (1) |
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List of Acronyms and Abbreviations |
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17 | (1) |
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18 | (1) |
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18 | (7) |
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2 Impacts of Histone Lysine Methylation on Chromatin |
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25 | (30) |
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Chromatin Regulation and Posttranslational Modifications |
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26 | (1) |
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Histone Lysine Methyltransferases |
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27 | (1) |
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28 | (3) |
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31 | (2) |
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Histone H3K27 Methylation |
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33 | (2) |
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Histone H3K36 Methylation |
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35 | (1) |
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Histone H3K79 Methylation |
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36 | (2) |
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Histone H4K20 Methylation |
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38 | (1) |
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Monomethylation of H4K20 Promotes Mitotic Chromatin Condensation and DNA Replication |
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39 | (1) |
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Emerging Roles of Non-Canonical Histone Lysine Methylation |
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40 | (1) |
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41 | (1) |
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List of Acronyms and Abbreviations |
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42 | (1) |
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42 | (13) |
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3 The Role of Histone Mark Writers in Chromatin Signaling: Protein Arginine Methyltransferases |
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55 | (20) |
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55 | (1) |
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General Properties of Protein Arginine Methyltransferases |
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56 | (5) |
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Mammalian Protein Arginine Methyltransferases and Their Effects on Gene Expression |
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61 | (9) |
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70 | (1) |
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List of Acronyms and Abbreviations |
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70 | (1) |
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71 | (1) |
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71 | (1) |
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71 | (4) |
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4 Histone Kinases and Phosphatases |
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75 | (22) |
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75 | (1) |
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Histone Phosphorylation: Basic Concepts |
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75 | (3) |
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Histone Kinases in Nucleosome Packing and Assembly |
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78 | (1) |
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Histone Kinases and Cell Division |
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78 | (4) |
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Histone Kinases in DNA Repair and Replication |
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82 | (1) |
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Histone Kinases and Programmed Cell Death |
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83 | (1) |
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Histone Kinases and Transcription |
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84 | (3) |
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87 | (1) |
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88 | (1) |
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List of Acronyms and Abbreviations |
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88 | (1) |
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89 | (1) |
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89 | (8) |
| II Histone Mark Readers |
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5 The Bromodomain as an Acetyl-Lysine Reader Domain |
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97 | (16) |
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Lysine Acetylation and the Bromodomain |
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97 | (1) |
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Discovery of the Bromodomain as an Acetyl-Lysine Recognition Module |
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98 | (2) |
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Biological Functions of Bromodomain Proteins |
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100 | (4) |
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Bromodomain Proteins in Human Disease Pathways |
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104 | (1) |
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Small Molecular Inhibitors of Bromodomains |
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104 | (3) |
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107 | (1) |
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List of Acronyms and Abbreviations |
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108 | (1) |
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108 | (1) |
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108 | (5) |
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113 | (14) |
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113 | (1) |
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The Chromo Domain Structure |
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114 | (1) |
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Varieties of Chromo Domains |
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114 | (3) |
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117 | (1) |
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Nucleic Acid-Binding Chromo Domains |
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117 | (1) |
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Posttranslational Modifications and Chromo Domain Transactions |
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118 | (1) |
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Targeting Chromo Domains for Therapeutics |
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119 | (1) |
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Chromo Domain Association With Human Disease |
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120 | (1) |
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121 | (1) |
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List of Acronyms and Abbreviations |
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121 | (1) |
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122 | (1) |
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122 | (5) |
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7 The Role of PHD Fingers in Chromatin Signaling: Mechanisms and Functional Consequences of the Recognition of Histone and Non-Histone Targets |
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127 | (22) |
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128 | (1) |
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The History of the Plant Homeodomain Finger |
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128 | (1) |
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The Structural Basis of Histone Recognition |
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128 | (4) |
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The Mechanism of Plant Homeodomain Fingers in the Combinatorial Readout of Patterns of Histone Post-Translational Modifications |
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132 | (5) |
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137 | (1) |
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Understanding the Role of the Plant Homeodomain Finger in the Function of Its Host Protein |
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138 | (2) |
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Plant Homeodomain Fingers in Disease |
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140 | (2) |
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142 | (1) |
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143 | (6) |
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8 Tudor Domains as Methyl-Lysine and Methyl-Arginine Readers |
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149 | (20) |
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149 | (1) |
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The Aromatic Cage: Molecular Basis of Methyl-Lysine and Methyl-Arginine Recognition |
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150 | (2) |
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Tudor Domains Interacting With Methylated Lysine-Containing Peptides |
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152 | (6) |
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Tudor Domains Interacting With Methylated Arginine-Containing Peptides |
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158 | (2) |
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160 | (1) |
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161 | (1) |
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161 | (8) |
| III Histone Mark Erasers |
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9 Histone Deacetylases, the Erasers of the Code |
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169 | (10) |
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169 | (1) |
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Histone Modifications and Gene Transcription |
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170 | (1) |
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Histone Deacetylase Families and Classes |
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171 | (1) |
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Histone Deacetylases Structures and Catalytic Mechanisms |
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172 | (1) |
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Histone Deacetylases as Modulators of the Epigenome |
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172 | (2) |
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Histone Deacetylases Biology |
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174 | (2) |
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176 | (1) |
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176 | (1) |
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176 | (3) |
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10 Lysine Demethylases: Structure, Function, and Disfunction |
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179 | (18) |
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179 | (1) |
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Families: Functional and Structural Features |
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180 | (2) |
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Transcriptional Output and Regulation |
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182 | (2) |
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184 | (2) |
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186 | (3) |
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KDM Inhibitors as New Epigenetic Drugs |
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189 | (2) |
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191 | (1) |
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191 | (1) |
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191 | (6) |
| IV Chromatin Signaling |
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11 Variation, Modification, and Reorganization of Broken Chromatin |
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197 | (20) |
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197 | (1) |
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Histone Modifications in DSB Repair |
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198 | (3) |
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Histone Variants in DSB Repair |
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201 | (4) |
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Chromatin Remodeling Enzymes in DSB Repair |
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205 | (6) |
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211 | (1) |
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211 | (6) |
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12 Crosstalk Between Histone Modifications Integrates Various Signaling Inputs to Fine-Tune Transcriptional Output |
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217 | (24) |
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217 | (1) |
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Crosstalk Between Histone Modifications and Their Consequences |
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218 | (1) |
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Histone Marks and Recruitment of Chromatin Factors |
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218 | (3) |
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Histone Lysine Methylation and Acetylation |
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221 | (1) |
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Histone Ubiquitination and Methylation: a Trans Effect |
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222 | (2) |
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224 | (2) |
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Histone-Modifying Complexes Have Multiple Catalytic Roles and Functions |
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226 | (3) |
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Histone Arginine Methylation |
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229 | (1) |
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Histone Tail Cleavage Exhibits the Ultimate Irreversible Removal of Histone Modifications |
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230 | (1) |
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Histone Modification at Enhancers |
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231 | (1) |
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231 | (1) |
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List of Acronyms and Abbreviations |
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232 | (3) |
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235 | (1) |
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235 | (6) |
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13 Signaling and Chromatin Networks in Cancer Biology |
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241 | (16) |
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241 | (1) |
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Regulation of Epithelial-Mesenchymal-Transition |
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242 | (1) |
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Chromatin Remodeling in the Regulation of Cancer Cell Plasticity |
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243 | (2) |
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The Epithelial-Mesenchymal-Transition Transcription Factor Machinery |
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245 | (4) |
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The Role of Posttranscriptional Regulation of Epithelial-Mesenchymal-Transition |
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249 | (1) |
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249 | (1) |
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250 | (7) |
| V Chromatin Dynamics In Normal And Disease Conditions |
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14 Crosstalk Between DNA Methylation and Chromatin Structure |
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257 | (14) |
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257 | (2) |
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Crosstalk Between DNA Methylation and Chromatin Structure |
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259 | (5) |
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Significance of Altered DNA-Chromatin Crosstalk in Disease |
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264 | (3) |
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267 | (1) |
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267 | (1) |
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268 | (3) |
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15 Epigenetic Regulation of Endoplasmic Reticulum Stress |
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271 | (16) |
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271 | (10) |
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281 | (1) |
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282 | (1) |
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282 | (1) |
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282 | (5) |
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16 Chromatin Signaling in Aging and Cellular Senescence |
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287 | (24) |
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Aging, Cellular Senescence, and Chromatin: an Introduction |
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288 | (2) |
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Nucleosomal Modifications in Senescence and Aging |
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290 | (3) |
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Histone Posttranslational Modifications During Cellular Senescence and Aging |
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293 | (4) |
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Modulation of Lifespan by Experimental Alteration of Chromatin Modifiers in Animal Models |
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297 | (3) |
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Age-Dependent Regulation of the Chromatin-Metabolism Connection |
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300 | (1) |
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Effect of Telomere Shortening on Telomeric Chromatin |
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301 | (1) |
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302 | (1) |
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List of Acronyms and Abbreviations |
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303 | (1) |
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303 | (8) |
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17 Chromatin Dynamics and Epigenetics of Stem Cells and Stem-Like Cancer Cells |
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311 | (18) |
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311 | (1) |
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312 | (1) |
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312 | (1) |
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Histone Modifications and Variants |
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313 | (1) |
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314 | (3) |
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Chromatin Dynamics During Embryo Development |
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317 | (1) |
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Chromatin Dynamics During Lineage Differentiation |
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317 | (1) |
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Cancer Stem-Like Cells: Historical Perspective |
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318 | (2) |
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Epigenetic Factors Regulating Tumorigenesis and Cancer Stem Cells |
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320 | (1) |
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Histone Modifications and Variants in CSCs |
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320 | (2) |
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Chromatin Remodeling in CSCs |
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322 | (2) |
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324 | (1) |
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324 | (5) |
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18 Altered Chromatin Signaling in Cancer |
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329 | (18) |
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329 | (2) |
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331 | (1) |
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332 | (9) |
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Metabolic Regulation of Epigenetic Signaling |
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341 | (1) |
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342 | (1) |
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342 | (5) |
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19 Impact of Chromatin Changes in Pathogenesis of Infectious Diseases: A Pathogen View |
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347 | (18) |
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347 | (8) |
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355 | (4) |
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359 | (1) |
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360 | (5) |
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20 Chromatin Remodeling and Epigenetic Reprogramming in Chronic Disease and Cancer in the Liver and Pancreas |
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365 | (22) |
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365 | (1) |
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Development of Pancreas and Liver |
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366 | (3) |
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Epigenetics of Liver Diseases |
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369 | (5) |
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Epigenetics of Pancreatic Diseases |
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374 | (5) |
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Future Directions: Clinical Potential of Targeting Chromatin-Remodeling Proteins |
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379 | (1) |
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380 | (1) |
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380 | (7) |
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21 Pharmacological and Therapeutic Targeting of Epigenetic Regulators |
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387 | (16) |
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387 | (1) |
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Targeting the DNA Methylation Pathway |
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388 | (2) |
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390 | (1) |
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Histone Acetylases and Deacetylases |
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391 | (3) |
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Histone Methylases and Demethylases |
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394 | (4) |
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398 | (1) |
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399 | (1) |
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400 | (3) |
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22 Use of Chromatin Changes as Biomarkers |
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403 | (20) |
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403 | (4) |
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Concept 1: Altered DNA Methylation Landscapes as Biomarkers of Human Disease |
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407 | (2) |
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Concept 2: Aberrant microRNA Expression in Disease States |
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409 | (3) |
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Concept 3: Disease-Specific Histone Posttranslational Modifications Function as Biomarkers |
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412 | (1) |
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Concept 4: Tissue Surrogate Epigenetic Biomarkers |
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413 | (3) |
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416 | (1) |
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List of Acronyms and Abbreviations |
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417 | (1) |
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418 | (1) |
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418 | (1) |
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418 | (5) |
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23 Regulation of Host Chromatin by Bacterial Metabolites |
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423 | (20) |
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423 | (1) |
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The Commensal Bacterial Metabolome |
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424 | (1) |
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Dietary Carcinogens Alter Chromatin |
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424 | (1) |
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Bile Acids: Microbial Bile-Ome and Nuclear Receptors |
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425 | (1) |
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Estrogens: Microbial Estrabolome and Chromatin Modulation |
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426 | (1) |
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Ellagic Acid and Histones Methylation |
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426 | (1) |
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Short Chain Fatty Acids (SCFAs), G Protein-Coupled Receptors, and Histone Deacetylases |
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426 | (1) |
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Indoles and Nuclear Receptors |
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427 | (3) |
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430 | (1) |
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431 | (1) |
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431 | (1) |
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431 | (1) |
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432 | (1) |
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Lessons to Apply from Host Intermediary Metabolism and Chromatin |
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432 | (1) |
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Metabolite Mining for Chromatin Modulation |
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433 | (2) |
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435 | (1) |
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List of Acronyms and Abbreviations |
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435 | (1) |
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435 | (8) |
| Index |
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443 | |