The Regulatory Genome

1st Edition

Gene Regulatory Networks In Development And Evolution

Authors: Eric Davidson
Hardcover ISBN: 9780120885633
eBook ISBN: 9780080455570
Imprint: Academic Press
Published Date: 30th May 2006
Page Count: 304
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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.

Key Features

  • The only book in the market that is solely devoted to the genomic regulatory code for animal development
  • Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding
  • Presents a comprehensive treatment of molecular control elements that determine the function of genes
  • Provides a comparative treatment of development, based on principles rather than description of developmental processes
  • Considers the evolutionary processes in terms of the structural properties of gene regulatory networks
  • Includes 42 full-color descriptive figures and diagrams


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.

Table of Contents

CHAPTER 1 The "Regulatory Genome" for Animal Development


THE REGULATORY APPARATUS ENCODED IN THE DNA Genomes, Genes, and Genomic "Space" Overview of Regulatory Architecture Gene Regulatory Networks

THE REGULATORY DEMANDS OF DEVELOPMENT Readout and Generation of Regulatory Information in Development; Specification Spatial Gene Expression From Regional Specification to Terminal Differentiation


CHAPTER 2 cis-Regulatory Modules, and the Structure/Function Basis of Regulatory Logic



INSIDE 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 Code

cis-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 Development

CONTROL 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 Looping

CHAPTER 3 Development as a Process of Regulatory State Specification



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© Academic Press 2006
Academic Press
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About the Author

Eric Davidson

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.

Affiliations and Expertise

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


"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