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Epigenetics

Linking Genotype and Phenotype in Development and Evolution

Benedikt Hallgrimsson Ph.D.

Publication Year: 2011

Illuminating the processes and patterns that link genotype to phenotype, epigenetics seeks to explain features, characters, and developmental mechanisms that can only be understood in terms of interactions that arise above the level of the gene. With chapters written by leading authorities, this volume offers a broad integrative survey of epigenetics. Approaching this complex subject from a variety of perspectives, it presents a broad, historically grounded view that demonstrates the utility of this approach for understanding complex biological systems in development, disease, and evolution. Chapters cover such topics as morphogenesis and organ formation, conceptual foundations, and cell differentiation, and together demonstrate that the integration of epigenetics into mainstream developmental biology is essential for answering fundamental questions about how phenotypic traits are produced.

Published by: University of California Press

Title Page, Copyright

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pp. 2-5

Contents

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pp. v-vi

Contributors

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pp. vii-viii

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1. Introduction

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pp. 1-6

Epigenetics is the study of emergent properties in the origin of the phenotype in development and in modification of phenotypes in evolution. Features, characters, and developmental mechanisms and processes are epigenetic if they can be understood only in terms of interactions that arise above the level of the gene as a sequence of DNA. ...

Part I: Historical and Philosophical Foundations

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2. A Brief History of the Term and Concept Epigenetics

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pp. 9-13

This chapter provides a brief evaluation of the history of epigenetics as a term and as a concept. Although the term was not coined until the 1940s, the concept that genes are influenced by factors beyond the genome (the “epi” in epigenetics) is much older and can be traced to late nineteenth-century discussions ...

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3. Heuristic Reductionism and the Relative Significance of Epigenetic Inheritance in Evolution

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pp. 14-40

The role of epigenetic inheritance in evolution is hotly contested. Some claim that recently discovered epigenetic mechanisms of gene regulation constitute a nongenetic inheritance system that underwrites a “Lamarckian dimension” of inheritance and therefore of evolution. ...

Part II: Approaches to Epigenetics

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4. The Epigenetics of Genomic Imprinting: Core Epigenetic Processes Are Conserved in Mammals, Insects, and Plants

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pp. 43-69

Genomic imprinting is an epigenetic process in which an allele is marked according to the sex of the parent transmitting it. These sex-specific marks may affect single genes, gene clusters, or entire chromosomes and result in maternal and paternal alleles or chromosomes that are epigenetically distinct from one another. ...

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5. Methylation Mapping in Humans

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pp. 70-86

The importance of DNA methylation mapping in humans was rapidly recognized once it became apparent that 5-methylcytosine (5mC) is not only an exotic and negligible modification of the DNA but an important carrier of epigenetic information. ...

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6. Asexuality and Epigenetic Variation

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pp. 87-102

Epigenetic processes are of fundamental importance for all living organisms as an individual phenotype is shaped by both its genome and its epigenome (Richards, 2006; Bossdorf et al., 2008). By epigenetic, we mean all molecular signals that are literally on top of DNA, such as cytosine methylation, chromatin marks, histone modification, and RNAi ...

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7. Epigenesis, Preformation, and the Humpty Dumpty Problem

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pp. 103-115

Humpty Dumpty, of nursery rhyme fame, was an egg that fell off a wall and “all the King’s horses and all the King’s men, couldn’t put Humpty together again.” If we think of an incubated fertilized hen’s egg maintained under proper conditions of temperature, humidity, and egg rolling, a chick will develop in a few weeks. ...

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8. A Principle of Developmental Inertia

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pp. 116-134

Biology has long suffered from comparison with physics—biology is largely concerned with the description of historically determined phenomena, rather than with eternal laws. Recently, however, the status of biology has increased substantially, largely because of its success in studying genes and their expression ...

Part III: Epigenetics of Vertebrate Organ Development

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9. The Role of Epigenetics in Nervous System Development

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pp. 137-163

A fundamental question is how cells acquire their specific identities and functional properties during embryogenesis. The intricate molecular controls that guide progression from pluripotent stem cells, which make up the early embryo, to a differentiated cell with a unique identity have begun to be elucidated (Figure 9.1). ...

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10. Morphogenesis of Pigment Patterns: Experimental and Modeling Approaches

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pp. 164-180

I used to live in Uppsala, Sweden, and would watch the jackdaws fly around in large flocks in the city center. The flock gives the impression of having a life of its own, of being a superorganism where the individual birds are the cells in the organism. ...

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11. Epigenetic Interactions of the Cardiac Neural Crest

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pp. 181-194

Epigenetic interactions as envisioned by Waddington involved animal, tissue, or cell responses to environmental cues such as hormones, cell–cell interactions, and mechanical and electrical forces. These mechanisms shape the “landscape” a cell travels through to reach its final differentiated state. ...

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12. Epigenetics in Bone and Cartilage Development

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pp. 195-220

This chapter describes the epigenetic processes involved in bone and cartilage development (osteogenesis and chondrogenesis, respectively). As defined earlier in this book, features, characters, or developmental processes are epigenetic if they can be understood only in terms of interactions that occur above the gene level. ...

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13. Muscle–Bone Interactions and the Development of Skeletal Phenotype: Jaw Muscles and the Skull

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pp. 221-237

The association between the musculature and the skeleton is both physiological and physical. Cell origins for the two tissues are not identical. For example, the cranial neural crest forms much of the skull but contributes only connective tissue to the muscles (Noden and Trainor, 2005). ...

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14. Evolution of the Apical Ectoderm in the Developing Vertebrate Limb

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pp. 238-255

Vertebrate limbs display a diverse array of morphologies, including the fins of teleosts and lungfish, wings of birds and bats, arms of humans, and flippers of cetaceans. Due to this morphological diversity, limbs are a topic of intense study in paleontology, phylogenetic systematics, descriptive embryology, ...

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15. Role of Skeletal Muscle in the Epigenetic Shaping of Organs, Tissues, and Cell Fate Choices

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pp. 256-268

Since the inception of my independent laboratory in July 2000, I have been able to study the role of muscle in the shaping of developing tissues, which is an important example of Waddington epigenetics. This has been the focus of my research program. ...

Part IV: Epigenetics in Evolution and Disease

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16. Epigenetic Integration, Complexity, and Evolvability of the Head: Rethinking the Functional Matrix Hypothesis

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pp. 271-289

As I get older, I find myself increasingly hesitant to use the word em>epigenetics because I worry about employing a term that is so liable to engender confusion and disagreement. Many biologists define epigenetics in a narrow sense solely as heritable changes in the phenotype that derive from molecular mechanisms ...

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17. Epigenetic Interactions: The Developmental Route to Functional Integration

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pp. 290-316

Epigenetic interactions are obviously necessary for normal development—without them there would be no primary embryonic induction, no epithelial–mesenchymal interactions, and no interactions between differentiated tissues such as muscles and bones. ...

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18. Epigenetic Contributions to Adaptive Radiation: Insights from ThreeSpine Stickleback

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pp. 317-336

Phenotypic plasticity is variation in trait expression caused by influences of the environment on the expression of the phenotype. Plasticity can buffer organisms against the exigencies of environmental variation, enhancing fitness and facilitating the persistence of populations in novel environments ...

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19. Learning, Developmental Plasticity, and the Rate of Morphological Evolution

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pp. 337-356

Much has been written about how learning— the developmental plasticity of behavior—and morphological plasticity—the developmental plasticity of form—may individually affect the rate of morphological evolution (reviewed in Maynard Smith, 1987; Pigliucci, 2001; Weber and Depew, 2003; West-Eberhard, 2003). ...

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20. Epigenetics: Adaptation or Contingency

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pp. 357-376

Living organisms are enormously complex. Through development, the complex phenotype is built by cells using the genetic information encoded in some billions of base pairs of genome. This process is amazingly accurate. ...

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21. The Epigenetics of Dysmorphology: Craniosynostosis as an Example

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pp. 377-397

Important discoveries in the field of evolutionary developmental biology have added significantly to our understanding of the evolution of developmental processes and the production of novel phenotypes, thereby advancing our knowledge of the molecular bases of genetic disease. ...

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22. Epigenetics of Human Disease

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pp. 398-423

Research into the ways in which vulnerability to chronic noncommunicable disease in humans is governed by patterns of gene expression determined by molecular epigenetic marks established during development in large part follows from, and is closely linked to, the growing interest in the “developmental origins of health and disease” (DOHaD). ...

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23. Epigenetics: The Context of Development

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pp. 424-438

The term epigenetics was coined by Conrad Hal Waddington in 1957 as a merger of epigenesis with genetics. Waddington (1957) defined epigenetics as the causal control of development or the causal control of gene action, without reference to specific mechanisms. ...

Index

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pp. 439-459

Production Notes

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p. 469-469


E-ISBN-13: 9780520948822
Print-ISBN-13: 9780520267091

Page Count: 472
Publication Year: 2011

Research Areas

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Subject Headings

  • Phenotype.
  • Epigenesis.
  • Genetic regulation.
  • Developmental genetics.
  • Evolutionary genetics.
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