The Regulatory Genome
Gene Regulatory Networks In Development And Evolution
- 1st Edition - May 30, 2006
- Imprint: Academic Press
- Author: Eric H. Davidson
- Language: English
- Hardback ISBN:9 7 8 - 0 - 1 2 - 0 8 8 5 6 3 - 3
- Paperback ISBN:9 7 8 - 1 - 4 8 3 2 - 9 9 9 8 - 3
- eBook ISBN:9 7 8 - 0 - 0 8 - 0 4 5 5 5 7 - 0
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 re… Read more
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Request a sales quoteGene 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.
- 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.
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
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
- Edition: 1
- Published: May 30, 2006
- No. of pages (Hardback): 304
- No. of pages (eBook): 304
- Imprint: Academic Press
- Language: English
- Hardback ISBN: 9780120885633
- Paperback ISBN: 9781483299983
- eBook ISBN: 9780080455570
ED
Eric H. 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, USARead The Regulatory Genome on ScienceDirect