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The Regulatory Genome
 
 

The Regulatory Genome, 1st Edition

Gene Regulatory Networks In Development And Evolution

 
The Regulatory Genome, 1st Edition,Eric Davidson,ISBN9780120885633
 
 
 

  

Academic Press

9780120885633

9780080455570

304

235 X 191

A successor to Eric Davidson's 2001 text, Genomic Regulatory Systems.

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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

Description

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.

Readership

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.

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

View additional works by Eric H. Davidson

The Regulatory Genome, 1st Edition

CHAPTER 1
The "Regulatory Genome" for Animal Development


THE FRAMEWORK

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

EVOLUTION, DEVELOPMENT, AND THE REGULATORY GENOME

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


GENERAL OPERATING PRINCIPLES

MODULARITY, A GENERAL PROPERTY OF GENOMIC cis-REGULATORY CONTROL UNITS

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


DEVELOPMENTAL PROCESSES OF THE PREGASTRULAR EMBRYO
Vectorial Embryogenesis
Maternal Anisotropy and External Cues for Axial Polarity
Spatial Regulatory Complexity and Interblastomere Signaling
Territories

COMPARATIVE 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 Process

REGULATORY 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 State

BODY PLAN DEVELOPMENT AND THE ORGANISM

CHAPTER 4
Gene Regulatory Networks for Development: What They Are, How They Work, and What They Mean


GENERAL STRUCTURAL PROPERTIES OF DEVELOPMENTAL GENE REGULATORY NETWORKS
Gene Regulatory Networks from Different Perspectives: Subcircuits to Process
Diagrams
Qualitative Diversity of Network Components
Extensions

GENE 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 Embryo

NETWORKS 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 neurons

CONCLUDING REMARKS

CHAPTER 5
Gene Regulatory Networks: The Roots of Causality and Diversity in Animal Evolution


EVOLUTIONARY 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 Networks

BILATERIAN 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 Kernels

SUBPHYLETIC EVOLUTION OF BILATERIAN BODY PLANS: HOX GENES AS SOURCES OF LABILE NETWORK INPUT/OUTPUT SWITCHES
Diverse Functional Consequences of hox Gene Expression
Multiple Examples: Regional Repression and Installation of Patterning Output, and
the Evolutionary Diversification of Body Parts
Hox Gene Subnetworks and Spatial Evolution

METAZOAN ORIGINS AND GENE NETWORKS BEFORE KERNELS
"Deconstructing" Bilaterian Gene Regulatory Networks in Time
Concluding Reflection: the Principle of Animal Development and Evolution

Quotes and reviews

"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.
 
 

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