Book review: Epigenetics in all its glory
Posted by Development Book Reviews, on 29 December 2011
This book review originally appeared in Development. Melissa Mann reviews “Epigenetics: Linking Genotype and Phenotype in Development and Evolution” (Edited by Benedikt Hallgrímsson and Brian K. Hall).
Epigenetics: Linking Genotype and Phenotype in Development and Evolution Edited by Benedikt Hallgrímsson, Brian K. Hall University of California Press (2011) 472 pages ISBN 978-0520267091 (hardback), 978-0520948822 (eBook) £59/$68 (hardback), $85 (eBook)
Ask ten scientists their definition of epigenetics and you may get ten answers. In its simplest form, epigenetics can be defined as above (epi) the level of genes (genetics), and in the book entitled Epigenetics: Linking Genotype and Phenotype in Development and Evolution, the editors, Benedikt Hallgrímsson and Brian K. Hall, have assembled 23 chapters that collectively embody epigenetics as described by this broad definition. Although the book is organized into four parts, it can be distilled into three themes that each discusses a more detailed interpretation of the field: molecular epigenetics, classical epigenetics/epigenetic interactions, and epigenetic interactions and evolution.
In its modern molecular reiteration, epigenetics is defined as a change in gene activity without a change in DNA sequence. Most molecular definitions of epigenetics also include the idea of heritability, or memory of gene activity, through cell division. Here, epigenetic modifications modulate gene expression through DNA methylation, histone modifications, changes in chromatin structure, and effects of non-coding RNAs. This book includes five chapters on molecular epigenetics, covering various organisms and topics from asexual organisms in the study of epigenetic variation to epigenetics and human disease. One chapter highlights neural development in which cell-fate switches are intimately linked with epigenetic changes. For example, transition from a neural stem cell to a progenitor cell involves a switch in co-factor associations. In response to Notch effector molecules, the HES1 repressor complex is transformed into a HES1 activator complex, thereby inducing a progenitor cell fate. A different mechanism may be utilized in neuronal fate specification in the neocortex. Changes in DNA looping and nuclear matrix binding may specify an upper layer neocortical fate. This chapter describes the current understanding of various epigenetic mechanisms involved in neural cell fate decisions.
The second theme of the book is classical epigenetics or epigenetic interactions. It is referred to as classical because the term ‘epigenetics’ was first coined by Conrad Waddington in 1942. Waddington’s definition of epigenetics was ‘the branch of biology which studies the causal interactions between genes and their products which bring the phenotype into being’ (Waddington, 1942). In Chapter 7, Ellen Larsen and Joel Atallah introduce epigenesis as the gradual unfolding of structure and function during development and present the analogy of a fertilized hen’s egg that develops into a downy chick: scrambling the egg retains all the genetic material and yet there is no development. This exemplifies the point of epigenetic interactions that occur above the gene level. Here, epigenetic interaction is the umbrella term for cell migration, physical interaction among cells and tissues, mechanical forces, embryonic induction (including cell signalling and hormones), and interactions between cells and their intrinsic or extrinsic environment. All these interactions may play a role in generating the ‘epigenetic landscape’ through which a cell must transverse to reach its final differentiated state within a tissue or organ. These epigenetic interactions are discussed in nine chapters, each of which focuses on the development of a specific cell type, tissue or organ. One chapter describes the mechanical force of muscle activity on bone as an epigenetic stimulus for developmental change. Using the mammalian jaw as the model system, the effects of mechanical force (muscle force, bite force and compression load) on lower mandible condylar cartilage growth are explored. Evidence is presented for increasing force leading to shorter, wider condylar cartilage growth and decreasing force for longer, thinner condylar cartilage growth. This chapter illustrates mechanical forces on development as an epigenetic mechanism.
The third theme, covered by six chapters in this book, is epigenetic interactions as a framework for evolution. For example, one chapter focuses on the epigenetic integration of various head modules (brain, bone/cartilage, muscle, eyes, tongue, teeth, muscles, sinuses/cavities) in development and its variations during human craniofacial evolution. Another chapter discusses the concept of adaptive plasticity and genetic assimilation in evolutionary change, as exemplified by the phenotypic and behavioural changes in threespine sticklebacks in different ecotypes. In deep, nutrient-poor lakes, threespine sticklebacks have evolved long snouts with upturned mouths suitable for planktonic prey, have lost group cannibalistic behaviour and display conspicuous courtship displays. In shallow, nutrient-rich lakes, threespine sticklebacks have short snouts and wide mouths for feeding on benthic invertebrates, display group cannibalistic foraging and have inconspicuous courtship, consisting of dorsal pricking. This chapter explores the phenotypic plasticity of an ancestral population in response to novel environments and its role in influencing subsequent evolutionary change.
In all languages, including the language of biology, words and terms can evolve and, thus, their meaning can change. Over time, the modern molecular definition of ‘epigenetics’ has supplanted other definitions. In Epigenetics: Linking Genotype and Phenotype in Development and Evolution, Hallgrímsson and Hall provide a comprehensive selection of epigenetics in its many forms and appeal to the reader to accept a broader definition of epigenetics – one that includes all things epigenetic: not just molecular epigenetics, but also classical epigenetics and epigenetic interactions related to evolution. Importantly, the context inherently linked in these definitions of epigenetics is the complex and finely tuned choreography of development. In the not too distant future, we will probably find that these definitions are intimately linked. As stated by Root Gorelick, Manfred Laubichler and Rachel Massicotte in Chapter 6 ‘the molecular epigenetic signals [can be considered] the nuts and bolts underlying the classical epigenesis sensu Waddington’.
This book celebrates epigenetics in all its glory. As a first of its kind, I recommend this book to researchers and graduate students who want to widen their perspective of epigenetics and its role in development and evolution. Because of the division in meaning, this book does require the reader to switch gear depending on whether the chapter is on molecular or classical epigenetics. Furthermore, it is steeped in epigenetic, development and evolution terminology. This makes it less than suitable for the undergraduate student. However, this book would be an excellent resource for a graduate course in classical epigenetics, or epigenetic interactions and evolution.