Gene regulation, epigenetics and hormone signaling

Content: Preface XIII Volume I 1 Eukaryotic Gene Expression by RNA Polymerase II 1Geetha Durairaj, Shivani Malik, and Sukesh R. Bhaumik 1.1 Introduction 1 1.2 Transcriptional Initiation of RNA Polymerase II Genes 1 1.3 Transcriptional Elongation of RNA Polymerase II Genes 5 1.4 Transcriptional Termination of RNA Polymerase II Gene 8 1.5 Capping of mRNA at the 5\'-End 9 1.6 Processing of mRNA at the 3\'-End 10 1.7 Splicing of mRNA 11 1.8 Nuclear Export of mRNA for Translation 13 1.9 Conclusion 17 References 17 2 Epigenetic Code: Histone Modification, Gene Regulation, and Chromatin Dynamics 29Arunoday Bhan, Paromita Deb, and Subhrangsu S. Mandal 2.1 Introduction 29 2.2 Histone Modifications 31 2.2.1 Histone Acetylation and Deacetylation 31 2.2.2 Histone Lysine Methylation 33 2.3 Histone Lysine Demethylation 38 2.4 Histone Arginine Methylation 39 2.5 Histone Phosphorylation and Dephosphorylation 40 2.6 Histone ADP-Ribosylation 42 2.7 Histone Ubiquitination 43 2.8 \"Epigenetic Code\" Hypothesis and Conclusion 44 Acknowledgments 48 List of Abbreviations 48 References 49 3 Histone Lysine Methylation, Demethylation, and Hormonal Gene Regulation 59Yaling Huang, Briana Dennehey, and Xiaobing Shi 3.1 Introduction 59 3.2 The Enzymes That Catalyze Histone Lysine Methylation and Demethylation 60 3.2.1 Lysine Methyltransferases (KMTs) 61 3.2.2 Lysine Demethylases (KDMs) 75 3.3 Histone Lysine Methylation in Hormone Signaling 78 3.3.1 Hormone Receptor Classification 78 3.3.2 Estrogen Receptor-Like Subfamily 80 3.3.3 Thyroid Hormone Receptor-Like Subfamily 85 3.3.4 Retinoid X Receptor-Like Subfamily 86 3.3.5 Nerve Growth Factor 1B-Like Subfamily 87 3.3.6 Steroidogenic Factor-Like Subfamily 87 3.4 Perspectives 87 Acknowledgments 88 Abbreviations 88 References 89 4 The Role of HATs and HDACs in Cell Physiology and Disease 101Irene Santos-Barriopedro, Helena Raurell-Vila, and Alejandro Vaquero 4.1 Introduction 101 4.2 HATs and HDACs 102 4.2.1 HATs 102 4.2.2 HDACs 104 4.3 Acetylation/Deacetylation in Chromatin-Associated Functions 107 4.3.1 HATs, HDACs, and Transcription 107 4.3.2 Chromatin Structure and Heterochromatin 110 4.3.3 HATs and HDACs in DNA Repair 111 4.4 HATs and HDACs in Cell Physiology 113 4.4.1 Cell-Cycle Regulation 113 4.4.2 Apoptosis, Aging, and Senescence 115 4.4.3 Differentiation and Development 117 4.4.4 Metabolism 120 4.5 Associated Diseases 122 4.5.1 Cancer 123 4.5.2 Vascular Diseases 126 4.5.3 Neurodegenerative Diseases 127 4.5.4 Other Diseases 127 References 127 5 The Short and Medium Stories of Noncoding RNAs: microRNA and siRNA 137Arunoday Bhan, Paromita Deb, Milad Soleimani, and Subhrangsu S. Mandal 5.1 Introduction 137 5.2 MicroRNA 140 5.2.1 Discovery of miRNAs 140 5.2.2 Biogenesis of miRNA 141 5.2.3 Processing of miRNA and its Mechanism of Action 141 5.2.4 Functional Significance of miRNA 144 5.2.5 Association of miRNAs with Human Diseases and Cancer 148 5.3 Small Interfering RNA (siRNA) 151 5.3.1 Discovery of siRNAs 151 5.3.2 Biogenesis of siRNAs 152 5.3.3 Processing and Mechanism of Action of siRNAs 153 5.4 Piwi interacting RNA 154 5.5 Transcription Initiating RNAs (TiRNAs) 155 5.6 Small Nuclear RNAs (snRNAs) 155 5.7 Conclusion 156 Acknowledgments 157 Abbreviations 157 References 157 6 Long Noncoding RNA (lncRNA): Functions in Health and Disease 169Arunoday Bhan, Milad Soleimani, and Subhrangsu S. Mandal 6.1 Introduction 169 6.2 Classification of lncRNAs 170 6.3 LncRNA: Functions and Mechanisms of Action 171 6.3.1 LncRNA XIST and TSIX in Dosage Compensation and X-Inactivation 172 6.3.2 HOTAIR (HOX Antisense Intergenic lncRNA) in Gene Silencing 172 6.3.3 H19: Important in Genomic Imprinting and microRNA Biogenesis 175 6.3.4 ANRIL: Transcriptional Regulation of INK4A Locus 177 6.3.5 GAS5: Associated with Growth and Glucocorticoid Receptor-Mediated Signaling 177 6.3.6 TERRA (Telomeric Repeat-Containing RNAs) in Telomere Function 178 6.3.7 MEG3: Important Player in Genomic Imprinting 179 6.3.8 KCNQ1OT1/LIT1: Key Player in Genomic Imprinting 179 6.3.9 MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) 180 6.3.10 PCAT1 180 6.3.11 PCGEM1 180 6.4 LncRNAs in Cancer 181 6.5 LncRNAs in Reproduction 185 6.6 LncRNAs in Myogenesis 187 6.7 LncRNA in Cardiovascular Disease 189 6.8 LncRNAs in Embryonic Development and Segmentation 190 6.9 LncRNA in Central Nervous System 190 6.10 LncRNAs in Neurological Disorders 191 6.11 LncRNA in Immune System and Immunological Disorders 193 6.12 Roles of lncRNAs in Various Heritable Syndromes 194 6.13 Conclusion 195 Acknowledgments 196 Abbreviations 196 References 197 7 Histone Variants: Structure, Function, and Implication in Diseases 209Francisca Alvarez and Alejandra Loyola 7.1 Histone Variants: Structure 209 7.1.1 Histone Proteins Have Sequence Variants 209 7.1.2 Histones are Posttranslationally Modified 211 7.1.3 Nucleosome Structure 213 7.2 Implication in Diseases 219 Acknowledgments 221 References 221 8 Genomic Imprinting in Mammals: Origin and Complexity of an Epigenetically Regulated Phenomenon 227Elena de la Casa-Esperon 8.1 Introduction: First Evidences and Extent of Genomic Imprinting 227 8.1.1 The Discovery of Imprinted Gene Expression 227 8.1.2 How Many Imprinted Genes? 228 8.2 Imprinted Genes: Common Features and Diversity of Regulatory Mechanisms 229 8.2.1 Imprinted Domains and the Elements That Control Them 229 8.2.2 Imprinted Expression Can Be Regulated in Multiple Ways 231 8.3 Role of Imprinted Noncoding RNAs on Imprinting Control and Other Functions 233 8.4 Parent-of-Origin-Dependent Epigenetic Marks and the Role of Chromatin Modifications and Interactions in Imprinting 234 8.4.1 Origin and Function of Differentially Methylated Regions in Imprinted Domains 234 8.4.2 The Contribution of Histone Modifications to Imprinting Control 237 8.4.3 Nuclear Location and Diverse Types of Interactions May also Play a Role in the Regulation of Imprinted Genes 237 8.5 Imprinted Genes: Functions and Associated Diseases 238 8.5.1 Mutations and Epimutations of Imprinted Loci Result in Diverse Disorders 238 8.5.2 Consequences of Loss of Imprinting 239 8.6 Origin and Evolution of Imprinting 241 8.6.1 Why Is There Imprinting? 241 8.6.2 When and How Did Imprinted Expression Emerge at Diverse Genes? 244 8.7 Summary and Conclusion 246 Acknowledgments 247 References 247 9 Centromere and Kinetochore: Essential Components for Chromosome Segregation 259Shreyas Sridhar, Arti Dumbrepatil, Lakshmi Sreekumar, Sundar Ram Sankaranarayanan, Krishnendu Guin, and Kaustuv Sanyal 9.1 Introduction 259 9.1.1 Distinguishing Features of Mitosis 261 9.2 Centromeres 262 9.2.1 Diversity in Organization of DNA Elements Across Centromeres 263 9.3 Kinetochores 269 9.3.1 Kinetochore Architecture 270 9.3.2 Centromere DNA-Associated Layer 270 9.3.3 Microtubule Interacting Layer 272 9.3.4 Kinetochore Assembly 273 9.4 Neocentromere 276 9.4.1 Naturally Occurring Neocentromeres 276 9.4.2 Artificially Induced Neocentromeres 277 9.4.3 Factors Relating to Neocentromere/Centromere Formation 278 9.5 Conclusions 279 Acknowledgment 280 References 280 10 Nuclear Receptors and NR-coregulators: Mechanism of Action and Cell Signaling 289Arunoday Bhan and Subhrangsu S. Mandal 10.1 Introduction 289 10.2 Structures of Nuclear Receptors 292 10.3 Mode of Action of Nuclear Receptors 295 10.4 Nuclear Receptor Coregulators 297 10.4.1 NR-Coactivators 298 10.4.2 Corepressors 306 10.4.3 Noncoding RNA (ncRNA) as NR-Coregulators 308 10.5 NRs and NR-Coregulators in Human Diseases 308 10.6 NRs and NR-Coregulators as Drug Targets 310 10.7 Conclusion 313 Acknowledgments 313 Abbreviations 313 References 314 Volume II 11 Estrogen and Progesterone Receptor Signaling and Action 329Linda I. Perrotti 12 Gonadal Steroid Hormones and Brain Protection 355Meharvan Singh, Courtney Brock, Rebecca Cunningham, and Chang Su 13 Glucocorticoid Receptor-Mediated Signaling and Stress Metabolism 377Rosalie M. Uht and Shreyas Bhave 14 Targeting Androgen Signaling in Prostate Cancer 399Paul H. Chung, Preethi Ravindranathan, Bishoy A. Gayed, and Ganesh V. Raj 15 Role of Peroxisome Proliferator-Activated Receptors in Inflammation and Angiogenesis 417Suchismita Acharya 16 RAR/RXR-Mediated Signaling 457Jorg Mey 17 On the Trail of Thyroid Hormone Receptor Epigenetics 511Pradip K. Sarkar 18 Insulin Signaling, Epigenetics, and Human Diseases 541Ragitha Chruvattil, Muskaan Belani, Tushar P. Patel, and Sarita Gupta 19 Endocrine Disruptors and Epigenetics 577John D. Bowman, Shaikh Mizanoor Rahman, and Mahua Choudhury 20 Endocrine Disruptors: Mechanism of Action and Impacts on Health and Environment 607Paromita Deb and Subhrangsu S. Mandal Index 639