Epigenetics and Development

Series Page

Contributors

Preface

Chapter One. Mechanisms and Dynamics of Heterochromatin Formation During Mammalian Development

1 Introduction

2 Heterochromatin in the Early Embryo: A Rather Particular Environment

3 Mechanisms of Heterochromatin Establishment and Inheritance

4 Concluding Remarks

References

Chapter Two. Functions of DNA Methylation and Hydroxymethylation in Mammalian Development

1 Introduction

2 Enzymatic Players

3 Patterns of DNA Methylation and Hydroxymethylation During Development

4 Role of Cytosine Methylation in Genome Regulation

5 Emerging Functions of Cytosine Hydroxymethylation

6 Conclusions

References

Chapter Three. Epigenetic Marking of the Zebrafish Developmental Program

1 Introduction: Setting the Stage for the Zebrafish Developmental Gene Expression Program

2 Turning on Gene Expression at the MZT

3 DNA Methylation Changes During the MZT

4 Developmental Gene Expression Prepatterning by DNA Hypomethylation

5 Prepatterning Developmental Gene Expression by Modified Histones Before ZGA

6 Developmental Epigenetic Fate Map Through the MBT: A Path to Multivalency?

7 Transgenerational Inheritance or De Novo Deposition of Embryonic Epigenetic Marks? Two Models

8 Conclusions and Perspectives

References

Chapter Four. Chromatin Architectures and Hox Gene Collinearity

1 Introduction

2 Hox Gene Function and Genomic Organization

3 The Many Faces of Collinearity

4 Are Polycomb and Trithorax Mediators of Collinearity?

5 Downstream of Polycomb and Trithorax: A Compacted Chromatin Architecture

6 3D Chromatin Organization and Collinearity in Drosophila

7 A 3D Chromatin Timer for Vertebrate Collinearity?

8 A Regulatory Archipelago and Collinearity in Developing Digits

9 Clustering, Coating, Compaction, Compartmentalization, and Contacts: The Five C’s of Collinearity?

References

Chapter Five. Primordial Germ-Cell Development and Epigenetic Reprogramming in Mammals

1 Embryology

2 PGC Specification

3 Regulation of Germ-Cell Survival and Migration

4 Epigenetic Reprogramming

5 PGC Culture and Embryonic Germ-Cell Derivation

6 Conclusion

References

Chapter Six. Epigenetics and Development in Plants

1 Introduction

2 Plant Epigenomes: Components and Organization

3 Chromatin-Based Processes During Vegetative Development

4 The Central Role of Epigenetics in Plant Reproductive Development

5 Transgenerational Inheritance of Epigenetic Variation

6 Concluding Remarks and Future Outlook

References

Chapter Seven. Reprogramming and the Pluripotent Stem Cell Cycle

1 Introduction

2 The Embryonic Stem Cell Cycle

3 Methods for Restoring Pluripotency

4 Critical Stages and Events in Epigenetic Reprogramming

5 DNA Synthesis and Chromatin Remodeling in Reprogramming

6 Concluding Remarks

References

Chapter Eight. H3K9/HP1 and Polycomb

1 Introduction and Evolutionary Perspective

2 The H3K9/HP1 Pathway and Its Role in Development

3 Polycomb Repressive Pathways

4 Conclusion

References

Chapter Nine. Parental Epigenetic Asymmetry in Mammals

1 Introduction

2 Generating Asymmetric Nuclear-Based Information in Parental Gametes

3 Immediate Inheritance and Reinforcement of Parental Asymmetry in the One-Cell Zygote

4 Global Loss and Specific Retention of Parental Asymmetries During Preimplantation Development

5 Scarce Maintenance of Parental Epigenetic Asymmetry After Embryo Implantation and Throughout Adulthood

6 Conclusions

References

Index