Chromatin Regulation and Dynamics

1st Edition - October 25, 2016
Editor: Anita Göndör
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 0 3 3 9 5 - 1
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 0 3 4 0 2 - 6

Chromatin Regulation and Dynamics integrates knowledge on the dynamic regulation of primary chromatin fiber with the 3D nuclear architecture, then connects related processes… Read more

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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
Chapter 1: A Brief Introduction to Chromatin Regulation and Dynamics
- Abstract
- 1.1. Introduction to Basic Concepts of Chromatin Regulation
- 1.2. Epigenetic Phenomena: Heritability of Chromatin States During Cell Division
- 1.3. Reprogramming of Epigenetic States During Development and in Diseases
- 1.4. Early Period of Chromatin Research
- 1.5. Discovery of the Nucleosome and Nucleosome Positioning
- 1.6. Histone Modifications: Discovery and Function
- 1.7. Discovery of DNA Methylation: Functions and Cross Talk With Histone Modifications
- 1.8. Replication Timing: Potential Vehicle for Epigenetic Inheritance and Reprogramming
- 1.9. Chromatin Folding in 3D: Basic Principles of Genome Organization
- 1.10. Signal Integration at the Level of Chromatin
- 1.11. Outlook
- Abbreviations
- Acknowledgments
- Conflict of Interest
Chapter 2: Histone Modifications and Histone Variants in Pluripotency and Differentiation
- Abstract
- 2.1. Histones and the Regulation of Transcription
- 2.2. Histone PTMs and Variants During Development
- 2.3. Conclusions
- Abbreviations
- Acknowledgments
Chapter 3: Dynamics and Function of DNA Methylation During Development
- Abstract
- 3.1. Establishment of the DNA Methylation Landscape
- 3.2. DNA Methylation in CpG Rich Versus CpG Poor Regions
- 3.3. DNA Demethylation and Hydroxy- Methylation
- 3.4. DNA Methylation and Transcriptional Silencing
- 3.5. Interactions Between DNA Methylation and Histone Modifications
- 3.6. Non-CpG Methylation
- 3.7. Dynamics of DNA Methylation During Early Development
- 3.8. Aberrant DNA Methylation in Diseases
- 3.9. Conclusions
- Abbreviations
- Acknowledgments
Chapter 4: ATP-Dependent Chromatin Remodeling: From Development to Disease
- Abstract
- 4.1. Introduction
- 4.2. ATP-Dependent Chromatin Remodelers
- 4.3. Mechanism of Action and Targeting of ATP-Dependent Chromatin Remodeling Complexes
- 4.4. The Role of Chromatin Remodeling Complexes During Development
- 4.5. The Role of Chromatin Remodeling Complexes in Cancer
- 4.6. The Role of Chromatin Remodeling Complexes During Aging
- 4.7. Conclusions
- Abbreviations
- Acknowledgments
Chapter 5: Chromatin Dynamics During the Cell Cycle
- Abstract
- 5.1. Introduction
- 5.2. Chromatin Organization: The Chain of Nucleosomes Forms Higher Order Structures
- 5.3. The Two States of Chromatin During Interphase: Euchromatin Versus Heterochromatin
- 5.4. Posttranslational Histone Modifications: Writers, Readers, and Erasers
- 5.5. Differential Patterns of H1 and Core Histone Modifications During the Cell Cycle
- 5.6. Chromatin Organization and DNA Replication
- 5.7. The Histone H3 Variant CENP-A Establishes the Site for Kinetochore Assembly
- 5.8. Mitotic Condensation of Chromatin
- 5.9. Reestablishment of Interphase Chromatin
- 5.10. Retention of Basic Chromatin Organization During Mitosis
- 5.11. Conclusions
- Glossary
- Abbreviations
Chapter 6: Epigenetic Regulation of Replication and Replication Timing
- Abstract
- 6.1. The Nature of Replication Start Sites, Initiator Factors, and Their Potential Regulation
- 6.2. Complex Genomes are Structured Into Replication Timing Domains
- 6.3. Regulation of Replication Origins by Epigenetic Marks
- 6.4. Global Regulators of Replication Timing Act Through 3D Nuclear Organization
- 6.5. Interplay Between Inheritance of Chromatin Marks and Replication
- 6.6. Concluding Remarks
Chapter 7: Regulation of Cellular Identity by Polycomb and Trithorax Proteins
- Abstract
- 7.1. Introduction
- 7.2. Functions of PcG and TrxG Proteins During Development
- 7.3. Molecular Functions of PcG and TrxG Proteins
- 7.4. Mechanisms of PcG and TrxG Recruitment
- 7.5. Interplay of PcGs/TrxGs in the Propagation of Transcriptional States
- 7.6. Conclusions
- Glossary
- Abbreviations
Chapter 8: Interplay Between Chromatin and Splicing
- Abstract
- 8.1. Introduction
- 8.2. Interplay Between Splicing and Transcription
- 8.3. Chromatin Structure and its Impact on Splicing
- 8.4. New Insights on Epigenetic Regulation of Alternative Splicing
- 8.5. Beyond Chromatin Structure
- 8.6. Concluding Remarks
- Abbreviations
Chapter 9: Crosstalk Between Non-Coding RNAs and the Epigenome in Development
- Abstract
- 9.1. Introduction
- 9.2. Functional Roles of lncRNAs
- 9.3. Regulatory Mechanisms of lncRNA Expression
- 9.4. Therapeutic Applications of lncRNAs
- 9.5. Conclusions
- Abbreviations
Chapter 10: Epigenetic Regulation of Nucleolar Functions
- Abstract
- 10.1. Introduction
- 10.2. Assembly of the Nucleolus
- 10.3. Regulation of the RNA Pol I Machinery
- 10.4. Chromatin at rRNA Genes
- 10.5. Noncoding RNAs in the Structural and Functional Integrity of the Nucleolus
- 10.6. RNA Pol III Transcription
- 10.7. Chromatin Remodeling Complexes Affecting RNA Pol III Transcription
- 10.8. RNA Pol III and Transcription of Short Interspersed Repeat Elements
- 10.9. RNA Pol III Genes, Boundary Elements, and Insulator Function
- 10.10. Ribosomal Transcription and Diseases
Chapter 11: Chromatin Dynamics and DNA Repair
- Abstract
- 11.1. Introduction
- 11.2. Chromatin Dynamics and DNA Repair
- 11.3. Chromosome Mobility and the DDR
- 11.4. Site-Specific Analysis of DNA Damage and Chromatin
- 11.5. Histone Dynamics Following DNA Damage
- 11.6. Genome Organization and Chromosomal Translocations
- 11.7. Conclusions
- Glossary
- Abbreviations
Chapter 12: Regulation of Centromeric Chromatin
- Abstract
- 12.1. Centromere—An Essential Chromatin Domain for Accurate Chromosome Segregation
- 12.2. CENP-A—The Determinant of Centromere Identity
- 12.3. The Chromatin Environment—An Important Player in Centromere Regulation
- 12.4. Centromeric DNA—Superfluous or Needed for Centromere Identity?
- 12.5. CENP-A Loading and the Maintenance of Centromeric Chromatin
- 12.6. The Constitutive Centromere Associated Network (CCAN) and Its Contribution to Centromere Maintenance
- 12.7. Centromeric Chromatin and Its Role Outside of Centromeres
- 12.8. Centromeric Chromatin and Its Role in Cancer
- 12.9. Perspectives
- Glossary
- Abbreviations
- Acknowledgments
Chapter 13: Telomere Maintenance in the Dynamic Nuclear Architecture
- Abstract
- 13.1. Introduction
- 13.2. Telomere Maintenance
- 13.3. Telomere Structure and Function
- 13.4. Telomere Chromatin Organization
- 13.5. Telomere Chromatin Dynamics During the Cell Cycle
- 13.6. Telomere Shortening and Deprotection
- 13.7. Telomeric Chromatin Dynamics on the Path to Replicative Senescence
- 13.8. Telomeres in the 3D Space of the Nucleus
- 13.9. Conclusions
- Glossary
- Abbreviations
Chapter 14: Epigenetic Regulation of X-Chromosome Inactivation
- Abstract
- 14.1. X-Chromosome Inactivation: a Historical Background
- 14.2. Long Noncoding RNAs and XCI
- 14.3. Chromatin Modifications Regulating X-Chromosome Inactivation
- 14.4. XCI Status in Pluripotency and During Reprogramming
- 14.5. Chromosomal Dynamics and Subnuclear Localization of Xi
- 14.6. X-Linked Diseases and Cancer Connections
- 14.7. Future Directions and Open Questions
- Abbreviations
- Acknowledgments
Chapter 15: Interaction Between Cellular Metabolic States and Chromatin Dynamics
- Abstract
- 15.1. Introduction
- 15.2. Intermediary Metabolism Products as Substrates or Cofactors for Chromatin Modifications
- 15.3. Metabolism, Chromatin, and Disease
- 15.4. Crosstalk Between Metabolism and Chromatin: A Two-Way Street?
- 15.5. Nutrient-Induced Epigenetic Inheritance
- 15.6. Conclusions, Unanswered Questions, and Future Perspectives
- Abbreviations
- Acknowledgments
Chapter 16: Circadian Plasticity of Chromatin States
- Abstract
- 16.1. The Circadian Clock
- 16.2. Circadian Chromatin Transitions
- 16.3. Genome-Wide Changes in 3D Chromatin Organization
- 16.4. DNA-Methylation and the Circadian Clock
- 16.5. Conclusions
- Acknowledgments
Chapter 17: 3D Nuclear Architecture and Epigenetic Memories: Regulators of Phenotypic Plasticity in Development, Aging and Cancer
- Abstract
- 17.1. Introduction
- 17.2. 3D Genome Organization and Cell Identity
- 17.3. Compartmentalization of Nuclear Functions in 3D
- 17.4. Chromatin Mobility Between Nuclear Compartments and Phenotypic Plasticity
- 17.5. Deregulated 3D Genome Organization and Cancer Evolution
- 17.6. Deregulation of Heterochromatin Compartments During Senescence and Aging
- 17.7. Conclusions
- Abbreviations
- Acknowledgment
Index

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Anita Göndör