The Regulatory Genome

Gene Regulatory Networks In Development And Evolution


  • Eric Davidson, Norman Chandler Professor of Cell Biology, California Institute of Technology, Pasadena, CA, USA

Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market.
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Students, postdocs, and professionals in developmental biology, cell biology, etc. Will also appeal to computational scientists, bioengineers, biophysicists, as well as to biologists, geneticists, cell/molec biologists.


Book information

  • Published: May 2006
  • ISBN: 978-0-12-088563-3


"The Regulatory Genome offers evo-devo aficionados an intellectual masterpiece to praise or to pan but impossible to ignore. Although there is clearly still much to learn about the evolution of gene networks and how these in turn constrain evolution, Davidson has placed a cornerstone for the comparative analysis of gene regulatory networks. Further research in this rather fresh field promises to help delineate the links between development and evolution." — Detlev Arendt, Developmental Biology Programme, European Molecular Biology Laboratory, Germany in SCIENCE "...a highly informative book, provocative in the best sense of the word, and very much at the forefront of the field of developmental biology in the 'post-genomic' era. I recommend it highly to anyone interested in the subject." - Igor B. Dawid, Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, NIH, in THE FASEB JOURNAL "...Davidson does an excellent job of reducing the complexity of different developmental pathways and modes of embryonic development in diverse animal phyla to a set of simplified and logical concepts and principles. He provides excellent illustrations and experimental examples derived from several model organisms: nematode worms, fruitflies, sea urchins, tunicates and vertebrates of different sorts. What is especially attractive about the book are the regulatory networks drawn as simple wiring and computational diagrams. These go a long way towards explaining the basic regulatory logic and engineering principles of some of the most complex biological phenomena: animal development and the evolution of body forms. This book should be read by all biologists who want to understand how development and evolution take place and what governs the workings of genomes. I also recommend it to computer scientists and engineers who are interested in the budding field of computational biology, as reading it does not require an extensive background in developmental biology." - Michael Karin, University of California San Diego School of Medicine, in NATURE "Every step of [Eric Davidson's] logic is presented with examples to explain his idea, with beautiful, well-designed color figures. His concept of the significant roles of gene regulatory networks in development and evolution can be clearly understood using the aforementioned key terms....I strongly recommend this book to young scientists with multidisciplinary talents, who will advance the author’s idea of the regulatory genome into its next phase, a voyage into the sea of genome complexity...reading this book is a pleasure, as it allows us to touch the incredible spirit of a very tough scientist. Davidson has developed his idea of the gene regulatory network in development and evolution for more than 35 years and has raised it finally to the level of a real paradigm." - Nori Satoh, Department of Zoology, Kyoto University, Japan, in NATURE GENETICS "Prof. Davidson achieves a remarkable synthesis of key concepts in genomics, embryology, and evolutionary biology. He makes a persuasive case for the importance of regulatory networks in revealing the logic of complex developmental processes. The book is at the cusp of traditional disciplines in the biological sciences and the emerging field of computational biology. We finally have a book that reduces complex phenomena to basic principles, and then describes how these principles can explain among the most remarkable phenomena in nature: animal development and evolution." - Mike Levine, University of California, Berkeley, U.S.A. "Eric Davidson is one of the real pioneers in deciphering the mysteries of development...This is a milestone work that needs to be read by every biologist interested in development, evolution and a systems view of life — for it provides deep insights into each of these areas." — Lee Hood, Institute for Systems Biology, Seattle, WA, U.S.A. "Davidson's book is tightly written with an impressive coverage of the field...I don't see how one can grasp the rapidly changing views of gene regulation and its evolution without a close study of Davidson's book." — Douglas H. Erwin, National Museum of Natural History, Washington D.C., U.S.A.

Table of Contents

CHAPTER 1The "Regulatory Genome" for Animal DevelopmentTHE FRAMEWORKTHE REGULATORY APPARATUS ENCODED IN THE DNA Genomes, Genes, and Genomic "Space" Overview of Regulatory Architecture Gene Regulatory NetworksTHE REGULATORY DEMANDS OF DEVELOPMENT Readout and Generation of Regulatory Information in Development; Specification Spatial Gene Expression From Regional Specification to Terminal DifferentiationEVOLUTION, DEVELOPMENT, AND THE REGULATORY GENOMECHAPTER 2cis-Regulatory Modules, and the Structure/Function Basis of Regulatory LogicGENERAL OPERATING PRINCIPLESMODULARITY, A GENERAL PROPERTY OF GENOMIC cis-REGULATORY CONTROL UNITSINSIDE THE cis-REGULATORY MODULE: LOGIC PROCESSING AND INPUT/OUTPUT RELATIONS cis-Regulatory Logic Processors: Examples Target Site Occupancy and Transcriptional Output Generalization: The Combinatorial cis-Regulatory Logic Codecis-REGULATORY DESIGN Integration of Spatial Inputs at the cis-Regulatory Level Repression and the Diversity of cis-Regulatory Design cis-Regulatory Design and the Creation of Spatial Complexity in DevelopmentCONTROL BY SEQUENCE SPECIFIC INTERACTIONS AMONG DISTANT cis-REGULATORY ELEMENTS Development and Basal Transcription Apparatus Specificity Control Functions of Sequence-Specific, Intra- and Inter-Genic Genomic LoopingCHAPTER 3Development as a Process of Regulatory State SpecificationDEVELOPMENTAL PROCESSES OF THE PREGASTRULAR EMBRYO Vectorial Embryogenesis Maternal Anisotropy and External Cues for Axial Polarity Spatial Regulatory Complexity and Interblastomere Signaling TerritoriesCOMPARATIVE VIEW OF EMBRYONIC PROCESSES, AND THE ORGANIZATION OF THE UNDERLYING GENE REGULATORY NETWORKS Shallow Gene Regulatory Networks of Type 1 Embryos More Complex Forms of Embryonic ProcessREGULATORY STATE AND NETWORK CIRCUITRY IN BUILDING ADULT BODY PARTS Steps in the Postembryonic Developmental Process The Progenitor Field Concept Subdivision of the Progenitor Field Regulatory StateBODY PLAN DEVELOPMENT AND THE ORGANISMCHAPTER 4Gene Regulatory Networks for Development: What They Are, How They Work, and What They MeanGENERAL STRUCTURAL PROPERTIES OF DEVELOPMENTAL GENE REGULATORY NETWORKS Gene Regulatory Networks from Different Perspectives: Subcircuits to Process Diagrams Qualitative Diversity of Network Components ExtensionsGENE REGULATORY NETWORKS FOR EMBRYONIC DEVELOPMENT The Sea Urchin Endomesoderm Network Regulatory Gene Network for Specification of Mesoderm in the Xenopus Embryo Gene Regulatory Network Controlling Dorsal-Ventral Territorial Specification in the Drosophila EmbryoNETWORKS THAT CONTROL CONSTRUCTION OF COMPONENTS OF ADULT BODY PARTS Network Organization in the Specification of Pancreatic ƒÒ-cells Cell fate exclusion by microRNAs in a gene regulatory network controlling terminal differentiation in C. elegans taste neuronsCONCLUDING REMARKSCHAPTER 5Gene Regulatory Networks: The Roots of Causality and Diversity in Animal EvolutionEVOLUTIONARY IMPLICATIONS OF THE STRUCTURE AND FUNCTION OF GENE REGULATORY NETWORKS The Parts of Gene Regulatory Networks, and the Qualities of Evolutionary Change Linnaean Framework for the Evolutionary Consequences of Alterations in Gene Regulatory NetworksBILATERIAN KERNELS, PREDICTED AND REAL Caveats and a Caution Regional Specification in the Bilaterian Nervous System The Bilaterian Gut A Possible Pan-Bilaterian Kernel Underlying Specification of the Heart Progenitor Field Distribution of KernelsSUBPHYLETIC EVOLUTION OF BILATERIAN BODY PLANS: HOX GENES AS SOURCES OF LABILE NETWORK INPUT/OUTPUT SWITCHES Diverse Functional Consequences of hox Gene ExpressionMultiple Examples: Regional Repression and Installation of Patterning Output, and the Evolutionary Diversification of Body Parts Hox Gene Subnetworks and Spatial EvolutionMETAZOAN ORIGINS AND GENE NETWORKS BEFORE KERNELS"Deconstructing" Bilaterian Gene Regulatory Networks in Time Concluding Reflection: the Principle of Animal Development and Evolution