Genomic Control Process - Eric H. Davidson, Isabelle S. Peter

Genomic Control Process (eBook)

Development and Evolution

Eric H. Davidson, Isabelle S. Peter (Autoren)

eBook Download: PDF | EPUB

2015 | 1. Auflage
460 Seiten
Elsevier Science (Verlag)
978-0-12-404746-4 (ISBN)

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes.

This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development.

Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life
Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework
Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature
Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type
Demonstrates the causal power of system-level understanding of genomic control process

Conceptually organizes a constellation of complex and diverse biological phenomena
Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models
Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Isabelle S. Peter is Assistant Research Professor and Eric H. Davidson is Norman Chandler Professor of Cell Biology in the Division of Biology and Biological Engineering at the California Institute of Technology, Pasadena, California. Over the last seven years they have co-authored a series of works on experimental, conceptual and computational analyses of developmental gene regulatory networks, including their evolutionary significance. The discussions and conceptual explorations occasioned by this collaboration produced the new synthetic views encompassed in this book, building on decades of earlier work summarized in the 2001 and 2006 Academic Press books by Eric H. Davidson.

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Front Cover 1
IFC 3
GENOMIC CONTROL PROCESS 4
Copyright 5
About the Authors 6
Contents 8
Preface 10
Dedications 13
Chapter 1 - The Genome in Development 14
1. Views of Development 14
2. Levels of Control of Gene Expression: Transcriptional Regulation 17
3. Levels of Control of Gene Expression: Noncoding RNAs 23
4. Levels of Control of Gene Expression: Histone Modifications 31
5. The Regulatory Genome 44
REFERENCES 49
Chapter 2 - Gene Regulatory Networks 54
1. Introductory Overview of Developmental GRNs 55
2. Boolean Spatial Output 58
3. Regulatory States 61
4. Regulation in Cis 61
5. Module Choice 67
6. Transcriptional Dynamics 71
7. Historical Origins and Antecedents of GRN Theory 83
REFERENCES 86
Chapter 3 - Genomic Strategies for Embryonic Development 92
1. Common Principles of Embryonic Development 93
2. Phylogenetic Framework 106
3. Genomic Strategies of Control in Mode 1 Embryonic Processes 111
4. Genomic Strategies of Control in Mode 2 Embryonic Processes 128
5. Global Aspects of A/P Spatial Regulatory Patterning in the Syncytial Drosophila Blastoderm 133
REFERENCES 139
Chapter 4 - Genomic Control Processes in Adult Body Part Formation 146
1. Common Principles of Body Part Formation 147
2. Limbs in Amniotes 149
3. Fly Legs 161
4. Establishment of Spatial Regulatory States in Early Development of Fly and Mammalian Brains 167
5. The Vertebrate Heart 183
6. Spatial Regulatory State Subdivision in and Around the Drosophila Ocellus 191
7. The Vertebrate Gut 192
Chapter 5 - Genomic Strategies for Terminal Cell Fate Specification 214
1. Circumstances of Terminal Cell Fate Specification 214
2. Combinatorial Cis-Regulatory Definition of Differentiation Gene Batteries 216
3. Cell Type Specification in Multipotential Embryonic Precursors 225
4. A Comment on Stem Cells in Postembryonic Life 262
5. Modular Call-Up of Given Specification Processes in Multiple Developmental Contexts 264
REFERENCES 268
Chapter 6 - On the Modeling of Developmental Gene Regulatory Networks 278
1. Topological Network Models 280
2. ODE Models of Circuit Dynamics 304
3. Boolean Models of Network Logic 322
4. Conclusions 334
REFERENCES 335
Chapter 7 - Evolution of Bilaterian Animals: Processes of Change and Stasis in Hierarchical Developmental Gene Regulatory Networks 340
1. Introduction: Evolution by Genomic Change at Different Levels of GRN Hierarchy 341
2. Evolution of the Body Plan by Co-Optive Alteration of GRN Structure 356
3. GRN Stasis and Phylogeny 390
4. Trans-Phyletic Conservation of Cell Type-Specific Regulatory States 396
5. Bilaterian Evolution 405
REFERENCES 409
Gene Index 418
Subject Index 424

Preface

In our time, the sheer volume of published experimental measurements, their scope and technical sophistication, compounded with a proliferation of diverse approaches, objectives, and model systems, has made it particularly difficult to see the conceptual forest for the trees. Yet all of the elegant and sophisticated though disparate and unconnected data sets with which we are confronted represent biological output of the same fundamental operating principles. Each experimental system provides a different window which offers a pathway to these principles. In this book we provide a conceptual framework that we hope will make accessible the principles by which the genomic control system operates developmental and evolutionary process. This framework grows from the realization that the most fundamental causal principles in biology, which distinguish biology from all other sciences, emerge from the existence and function of genomic information. From the genomic sequence are to be recovered the determinants of body plan development in animals. Of course, the processes of biology are subject to the same laws of physics and chemistry as are those of the inanimate world, but it is the genome that mandates biological organization. This is not a metaphor, it is a description of mechanisms that we can now begin to perceive as an unbroken chain of causal connections, leading from the A’s, C’s, G’s and T’s of the genomic DNA to the developmental formulation of the elements of the organism.

The new field that is coalescing around the concepts of genomic information processing partakes of principles and evidence from systems biology, developmental molecular biology, various aspects of body plan evolution and phylogenetics, as well as biological engineering and computational modeling. We found it useful to select and incorporate insights from all of these fields, where these illuminate the genomic control of development, without operating wholly within the paradigms of any one of them. In this book we focus on the main characteristics of the genomic control system, which include its hierarchy, its logic processing functions and its structural organization in the form of gene regulatory networks. Such networks encompass at a system level the recognition interactions between transcription factors and DNA sequence that lie at the heart of the whole regulatory process. The general operational properties of genomic regulatory systems are shared across the Bilateria, while diversity in animal forms directly reflects diversity in genomic developmental programs. Focus on the genomic programs controlling development provides a single conceptual lens through which the most disparate phenomena of development and evolution can be viewed, causally understood and interpreted.

A brief précis of the trajectory of our treatment follows: Chapter 1 is about the molecular biology of sequence-dependent regulation of gene expression in animal development. Here we consider three major levels at which gene expression is controlled, with respect to their roles in the developmental process. The first is transcriptional regulation by sequence-specific transcription factors and their interaction with cis-regulatory modules. Secondly, miRNAs modulate transcript prevalence, and a third level operates by means of chromatin modifications installed upon transcription factor-DNA interactions. While the expression of many genes is affected successively by all these mechanisms, control of developmental complexity is executed by transcription factors and their sequence-specific interactions with the regulatory genome. We further conclude that the primary key to the informational process of development lies in the control system regulating the expression of genes encoding transcription factors.

Chapter 2 focusses on the transcriptional control apparatus that operates animal development. Gene regulatory network (GRN) theory defines the principal structural and functional properties of genomic control programs in animals. Here we provide an introductory overview, specifying the components of GRNs, and focusing on higher level design features such as hierarchy, modular organization, and the unidirectionality of these encoded regulatory systems. Two major aspects of GRN output are their generation of regulatory states that in turn determine all downstream genetic functions, and the Boolean nature of spatial gene expression. The genomic regulatory transactions linked together in GRNs are executed by cis-regulatory modules, and their combinatorial information processing functions deeply affect GRN organization. This Chapter further includes a first principles quantitative treatment of network dynamics, which rationalizes the measurable kinetics of accumulation of transcriptional products and permits computational assessment of the outputs of regulatory gene cascades. Current GRN theory devolves from multiple earlier roots which we very briefly trace.

Chapter 3 focusses on the means by which the transcriptional regulatory system is deployed in the pre-gastrular development of many kinds of bilaterian animal. The fundamental task in early embryogenesis is to install in the descendants of a single cell initial patterns of spatial regulatory gene expression in respect to the axes of the future body plan. This poses control challenges unlike any others encountered in bilaterian life. We introduce in this Chapter general principles of development couched in terms of regulatory logic, such as the regulatory properties of the egg, inductive signaling, differentiation and cellular morphogenesis. Beyond these, bilaterian evolution has given rise to several distinct developmental strategies for pre-gastrular embryogenesis, specifically those of regularly cleaving small embryos with early onset of transcription; of large embryos undergoing rapid cell division with delayed onset of transcription and cell motility; of embryos utilizing a transcriptionally active syncytium. Here, for each of these strategies, we focus on particular regulatory design features of GRNs encoding embryonic specification, response to maternal spatial inputs, territorial pattern formation, and global control of zygotic gene expression.

Chapter 4 is about animal body part development. Bilaterian body parts are formed during development according to a common scheme. The basic principles, irrespective of body part or organism, emerge from studies that reveal the genomically encoded mechanisms underlying body part formation. Here we consider partial gene regulatory networks that have been solved for a diverse variety of body parts including brains, hearts, limbs, and guts, in Drosophila and/or vertebrates. In all of these cases, the process of body part formation begins with the allocation of a progenitor field, defined by installation of an initial regulatory state, and its placement in respect to the axes of the body plan. There follows the progressively finer subdivision of this field into appropriately positioned regulatory state domains that generate the subparts and ultimately the cell types of the body part. Circuitry commonly encountered in these GRNs controls signaling interactions, exclusion functions and boundary formation, and often involves feedback and feed forward regulation.

Chapter 5 considers the differentiation of cell types as the final readout of the preceding spatial specification processes in development of the body plan. Cell types represent the installation of biological and molecular effector functions within the matrix of spatial regulatory states. Here the focus is on the specific genomically encoded wiring utilized for deployment of cohorts of effector genes in terminal differentiation. Two objectives require to be fulfilled: one is the regional activation and permanent maintenance of expression of a small set of driver regulatory genes; and the other is control of large sets of effector genes by these drivers. The first is accomplished by positive feedback circuitry among the driver genes, usually accompanied by exclusion of drivers of alternative cell fates, and the second depends on effector gene cis-regulatory architecture. Our examples include Drosophila photoreceptors, and differentiation of erythrocytes, somitic muscle, neural crest and placodes in vertebrates. Diverse body parts often deploy similar cell types and this is mediated by modularity of genomic regulatory systems.

In Chapter 6 we analyze diverse approaches to construction of quantitative and logic models of gene regulatory networks. The structural and functional properties of GRNs can be accessed only by use of models. In this Chapter we consider diverse forms of GRN model, focusing on insights into the biology of developmental GRNs that accrue from the generation of abstract mathematical, logical or topological models. Topological models provide genome-centered maps of regulatory linkages, and thus graphically represent the architecture of causal interaction networks. We address the significance of network topology in an extensive comparative structure/function analysis of GRN subcircuit architecture. Insights otherwise unattainable emerge from dynamical mathematical treatment of GRN function. We review informative applications of ODE analysis to developmental GRNs operating in Drosophila embryos and in mammalian hematopoietic cells, and consider the regulatory interpretation of morphogen gradients. We turn then to Boolean models which are focused on GRN logic transactions. Several asynchronous models are considered and we end with a summary of the new insights deriving from a comprehensive Boolean logic model of the sea urchin embryo...

Erscheint lt. Verlag	21.1.2015
Sprache	englisch
Themenwelt	Informatik ► Weitere Themen ► Bioinformatik
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
	Technik
ISBN-10	0-12-404746-7 / 0124047467
ISBN-13	978-0-12-404746-4 / 9780124047464

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Buch | Hardcover (2015)

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