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Göndör Anita (Ed.) Chromatin Regulation and Dynamics

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Göndör Anita (Ed.) Chromatin Regulation and Dynamics
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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