Chromatin Regulation and Dynamics

Anita Göndör

• Publisher: Academic Press
• Year: 2016
• Print ISBN: 9780128033951
• eBook ISBN: 9780128034026
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

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.- Presents and discusses novel principles of chromatin regulation and dynamics with a cross-disciplinary perspective- Promotes crosstalk between basic sciences and their applications in medicine- Provides a framework for future studies on complex diseases by integrating various aspects of chromatin biology with cellular metabolic states, with an emphasis on the dynamic nature of chromatin and stochastic principles- Integrates knowledge on the dynamic regulation of primary chromatin fiber with 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes

Chapter 1

A Brief Introduction to Chromatin Regulation and Dynamics

I. Tzelepis^a

M. Martino^a

A. Göndör Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden

Abstract

Chromatin modifications influence all the nuclear functions that are templated by the DNA, and regulate when and how the genome should be expressed and copied. As chromatin states are reversible in nature, elaborate mechanisms have evolved to ensure the stable inheritance and maintenance of chromatin states that define differentiation stage- and cell type–specific gene expression patterns. Importantly, these heritable marks, termed epigenetic modifications, can also be reprogrammed by environmental signals. The heritability and reversibility of chromatin modifications thus regulate developmental processes in multicellular organisms by balancing between the robust maintenance of the phenotype against environmental perturbations and phenptypic plasticity during adaptive responses. In this process chromatin has been envisaged to function as a platform for both buffering against and integrating environmental cues, enabling the propagation of transient signals over time. In this chapter we will discuss the brief history and recent advances of chromatin-based processes to provide an overview about the role of chromatin in development and the deregulation of these processes in diseases.

Keywords

epigenetic inheritance

chromatin states

3D nuclear architecture

cellular signaling

nuclear functions

development

complex diseases

Contents

1.1 Introduction to Basic Concepts of Chromatin Regulation

1.2 Epigenetic Phenomena: Heritability of Chromatin States During Cell Division

1.2.1 Inheritance of Stable, Cell Type–Specific Gene Expression Patterns

1.2.2 Genomic Imprinting

1.2.3 Random Monoallelic Gene Expression

1.2.4 Other Epigenetic Phenomena

1.3 Reprogramming of Epigenetic States During Development and in Diseases

1.3.1 Reprogramming of Epigenetic Marks During Early Development

1.3.2 Epigenetic Reprogramming in Tumor Development

1.4 Early Period of Chromatin Research

1.5 Discovery of the Nucleosome and Nucleosome Positioning

1.6 Histone Modifications: Discovery and Function

1.6.1 The Language of Histone Modifications

1.7 Discovery of DNA Methylation: Functions and Cross Talk With Histone Modifications

1.7.1 Discovery of DNA Methylation

1.7.2 DNA Methylation in Tumor Development

1.7.3 Cross Talk Between DNA Methylation and Histone Modifications

1.8 Replication Timing: Potential Vehicle for Epigenetic Inheritance and Reprogramming

1.9 Chromatin Folding in 3D: Basic Principles of Genome Organization

1.9.1 Cross Talk Between Regulatory Elements

1.9.2 Technical Innovations to Detect 3D Genome Organization

1.9.3 Compartmentalization of Nuclear Functions

1.10 Signal Integration at the Level of Chromatin

1.11 Outlook

Abbreviations

Acknowledgments

Conflict of Interest

References

1.1. Introduction to Basic Concepts of Chromatin Regulation

The distinct cell types of a multicellular organism have stable, characteristic phenotypes and perform specialized functions; despite that they contain, with few exceptions, the very same DNA sequence. The existence of a system that regulates the cell type–specific use of the genetic material and provides cellular memories of gene expression patterns over time has been long recogni...

Table of contents

• Cover
• Title page
• Table of Contents
• Copyright
• List of Contributors
• Preface
• Chapter 1: A Brief Introduction to Chromatin Regulation and Dynamics
• Chapter 2: Histone Modifications and Histone Variants in Pluripotency and Differentiation
• Chapter 3: Dynamics and Function of DNA Methylation During Development
• Chapter 4: ATP-Dependent Chromatin Remodeling: From Development to Disease
• Chapter 5: Chromatin Dynamics During the Cell Cycle
• Chapter 6: Epigenetic Regulation of Replication and Replication Timing
• Chapter 7: Regulation of Cellular Identity by Polycomb and Trithorax Proteins
• Chapter 8: Interplay Between Chromatin and Splicing
• Chapter 9: Crosstalk Between Non-Coding RNAs and the Epigenome in Development
• Chapter 10: Epigenetic Regulation of Nucleolar Functions
• Chapter 11: Chromatin Dynamics and DNA Repair
• Chapter 12: Regulation of Centromeric Chromatin
• Chapter 13: Telomere Maintenance in the Dynamic Nuclear Architecture
• Chapter 14: Epigenetic Regulation of X-Chromosome Inactivation
• Chapter 15: Interaction Between Cellular Metabolic States and Chromatin Dynamics
• Chapter 16: Circadian Plasticity of Chromatin States
• Chapter 17: 3D Nuclear Architecture and Epigenetic Memories: Regulators of Phenotypic Plasticity in Development, Aging and Cancer
• Index