Academic Press, 2017. — 496 p. — ISBN 9780128034026, 9780128033951.Chromatin Regulation and Dynamics integrates knowledge on the dynamic regulation of primary chromatin fiber with the 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes. The final chapters discuss the many ways chromatin dynamics can synergize to fundamentally contribute to the development of complex diseases.Chromatin dynamics, which is strategically positioned at the gene-environment interface, is at the core of disease development. As such, Chromatin Regulation and Dynamics, part of the Translational Epigenetics series, facilitates the flow of information between research areas such as chromatin regulation, developmental biology, and epidemiology by focusing on recent findings of the fast-moving field of chromatin regulation.List of Contributors Preface A Brief Introduction to Chromatin Regulation and Dynamics Abstract Introduction to Basic Concepts of Chromatin Regulation Epigenetic Phenomena: Heritability of Chromatin States During Cell Division Reprogramming of Epigenetic States During Development and in Diseases Early Period of Chromatin Research Discovery of the Nucleosome and Nucleosome Positioning Histone Modifications: Discovery and Function Discovery of DNA Methylation: Functions and Cross Talk With Histone Modifications Replication Timing: Potential Vehicle for Epigenetic Inheritance and Reprogramming Chromatin Folding in 3D: Basic Principles of Genome Organization Signal Integration at the Level of Chromatin Outlook Abbreviations Acknowledgments Conflict of Interest Histone Modifications and Histone Variants in Pluripotency and Differentiation Abstract Histones and the Regulation of Transcription Histone PTMs and Variants During Development Conclusions Abbreviations Acknowledgments Dynamics and Function of DNA Methylation During Development Abstract Establishment of the DNA Methylation Landscape DNA Methylation in CpG Rich Versus CpG Poor Regions DNA Demethylation and Hydroxy- Methylation DNA Methylation and Transcriptional Silencing Interactions Between DNA Methylation and Histone Modifications Non-CpG Methylation Dynamics of DNA Methylation During Early Development Aberrant DNA Methylation in Diseases Conclusions Abbreviations Acknowledgments ATP-Dependent Chromatin Remodeling: From Development to Disease Abstract Introduction ATP-Dependent Chromatin Remodelers Mechanism of Action and Targeting of ATP-Dependent Chromatin Remodeling Complexes The Role of Chromatin Remodeling Complexes During Development The Role of Chromatin Remodeling Complexes in Cancer The Role of Chromatin Remodeling Complexes During Aging Conclusions Abbreviations Acknowledgments Chromatin Dynamics During the Cell Cycle Abstract Introduction Chromatin Organization: The Chain of Nucleosomes Forms Higher Order Structures The Two States of Chromatin During Interphase: Euchromatin Versus Heterochromatin Posttranslational Histone Modifications: Writers, Readers, and Erasers Differential Patterns of H1 and Core Histone Modifications During the Cell Cycle Chromatin Organization and DNA Replication The Histone H3 Variant CENP-A Establishes the Site for Kinetochore Assembly Mitotic Condensation of Chromatin Reestablishment of Interphase Chromatin Retention of Basic Chromatin Organization During Mitosis Conclusions Glossary Abbreviations Epigenetic Regulation of Replication and Replication Timing Abstract The Nature of Replication Start Sites, Initiator Factors, and Their Potential Regulation Complex Genomes are Structured Into Replication Timing Domains Regulation of Replication Origins by Epigenetic Marks Global Regulators of Replication Timing Act Through 3D Nuclear Organization Interplay Between Inheritance of Chromatin Marks and Replication Concluding Remarks Regulation of Cellular Identity by Polycomb and Trithorax Proteins Abstract Introduction Functions of PcG and TrxG Proteins During Development Molecular Functions of PcG and TrxG Proteins Mechanisms of PcG and TrxG Recruitment Interplay of PcGs/TrxGs in the Propagation of Transcriptional States Conclusions Glossary Abbreviations Interplay Between Chromatin and Splicing Abstract Introduction Interplay Between Splicing and Transcription Chromatin Structure and its Impact on Splicing New Insights on Epigenetic Regulation of Alternative Splicing Beyond Chromatin Structure Concluding Remarks Abbreviations Crosstalk Between Non-Coding RNAs and the Epigenome in Development Abstract Introduction Functional Roles of lncRNAs Regulatory Mechanisms of lncRNA Expression Therapeutic Applications of lncRNAs Conclusions Abbreviations Epigenetic Regulation of Nucleolar Functions Abstract Introduction Assembly of the Nucleolus Regulation of the RNA Pol I Machinery Chromatin at rRNA Genes Noncoding RNAs in the Structural and Functional Integrity of the Nucleolus RNA Pol III Transcription Chromatin Remodeling Complexes Affecting RNA Pol III Transcription RNA Pol III and Transcription of Short Interspersed Repeat Elements RNA Pol III Genes, Boundary Elements, and Insulator Function Ribosomal Transcription and Diseases Chromatin Dynamics and DNA Repair Abstract Introduction Chromatin Dynamics and DNA Repair Chromosome Mobility and the DDR Site-Specific Analysis of DNA Damage and Chromatin Histone Dynamics Following DNA Damage Genome Organization and Chromosomal Translocations Conclusions Glossary Abbreviations Regulation of Centromeric Chromatin Abstract Centromere—An Essential Chromatin Domain for Accurate Chromosome Segregation CENP-A—The Determinant of Centromere Identity The Chromatin Environment—An Important Player in Centromere Regulation Centromeric DNA—Superfluous or Needed for Centromere Identity? CENP-A Loading and the Maintenance of Centromeric Chromatin The Constitutive Centromere Associated Network (CCAN) and Its Contribution to Centromere Maintenance Centromeric Chromatin and Its Role Outside of Centromeres Centromeric Chromatin and Its Role in Cancer Perspectives Glossary Abbreviations Acknowledgments Telomere Maintenance in the Dynamic Nuclear Architecture Abstract Introduction Telomere Maintenance Telomere Structure and Function Telomere Chromatin Organization Telomere Chromatin Dynamics During the Cell Cycle Telomere Shortening and Deprotection Telomeric Chromatin Dynamics on the Path to Replicative Senescence Telomeres in the 3D Space of the Nucleus Conclusions Glossary Abbreviations Chapter 14: Epigenetic Regulation of X-Chromosome Inactivation Abstract X-Chromosome Inactivation: a Historical Background Long Noncoding RNAs and XCI Chromatin Modifications Regulating X-Chromosome Inactivation XCI Status in Pluripotency and During Reprogramming Chromosomal Dynamics and Subnuclear Localization of Xi X-Linked Diseases and Cancer Connections Future Directions and Open Questions Abbreviations Acknowledgments Interaction Between Cellular Metabolic States and Chromatin Dynamics Abstract Introduction Intermediary Metabolism Products as Substrates or Cofactors for Chromatin Modifications Metabolism, Chromatin, and Disease Crosstalk Between Metabolism and Chromatin: A Two-Way Street? Nutrient-Induced Epigenetic Inheritance Conclusions, Unanswered Questions, and Future Perspectives Abbreviations Acknowledgments Circadian Plasticity of Chromatin States Abstract The Circadian Clock Circadian Chromatin Transitions Genome-Wide Changes in 3D Chromatin Organization DNA-Methylation and the Circadian Clock Conclusions Acknowledgments C3D Nuclear Architecture and Epigenetic Memories: Regulators of Phenotypic Plasticity in Development, Aging and Cancer Abstract Introduction D Genome Organization and Cell Identity Compartmentalization of Nuclear Functions in 3D Chromatin Mobility Between Nuclear Compartments and Phenotypic Plasticity Deregulated 3D Genome Organization and Cancer Evolution Deregulation of Heterochromatin Compartments During Senescence and Aging Conclusions Abbreviations Acknowledgment Index
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