The regulatory genome : gene regulatory networks in development and evolution / New ed.
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ISBN：9780120885633
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简介
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. Examplesof 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 thatdetermine 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.
目录
Preface p. ix
The "Regulatory Genome" for Animal Development p. 1
The Framework p. 1
The Regulatory Apparatus Encoded in the DNA p. 3
Genomes, Genes, and Genomic "Space" p. 3
Overview of Regulatory Architecture p. 8
Gene Regulatory Networks p. 11
The Regulatory Demands of Development p. 16
Readout and Generation of Regulatory Information in Developmental Specification p. 16
Spatial Gene Expression p. 18
From Regional Specification to Terminal Differentiation p. 21
Evolution, Development, and the Regulatory Genome p. 27
cis-Regulatory Modules, and the Structure/Function Basis of Regulatory Logic p. 31
General Operating Principles p. 31
Modularity, A General Property of Genomic cis-Regulatory Control Units p. 33
Inside the cis-Regulatory Module: Logic Processing and Input/Output Relations p. 47
cis-Regulatory Logic Processors: Examples p. 48
Target Site Occupancy and Transcriptional Output p. 57
Generalization: The Combinatorial cis-Regulatory Logic Code p. 59
cis-Regulatory Design p. 61
Integration of Spatial Inputs at the cis-Regulatory Level p. 61
Repression and the Diversity of cis-Regulatory Design p. 68
cis-Regulatory Design and the Creation of Spatial Complexity in Development p. 73
Control by Sequence-Specific Interactions Among Distant cis-Regulatory Elements p. 78
Development and BTA Specificity p. 79
Control Functions of Sequence-Specific, Intra- and Intergenic Genomic Looping p. 80
Development as a Process of Regulatory State Specification p. 87
Developmental Processes of the Pregastrular Embryo p. 87
Vectorial Embryogeniss p. 88
Maternal Anisotropy and External Cues for Axial Polarity p. 90
Spatial Regulatory Complexity and Interblastomere Signaling p. 94
Territories p. 100
Comparative View of Embryonic Processes, and the Organization of the Underlying Gene Regulatory Networks p. 102
Shallow Gene Regulatory Networks of Type 1 Embryos p. 103
More Complex Forms of Embryonic Process p. 109
Regulatory State and Network Circuitry in Building Adult Body Parts p. 114
Steps in the Postembryonic Developmental Process p. 114
The Progenitor Field Concept p. 115
Subdivision of the Progenitor Field Regulatory State p. 121
Body Plan Development and the Organism p. 122
Gene Regulatory Networks for Development: What They Are, How They Work, and What They Mean p. 125
General Structural Properties of Developmental Gene Regulatory Networks p. 126
Overall Network Structure p. 127
Gene Regulatory Networks from Different Perspectives: Subcircuits to Process Diagrams p. 135
Qualitative Diversity of Network Components p. 136
Extensions p. 140
Gene Regulatory Networks for Embryonic Development p. 144
The Sea Urchin Endomesoderm Network p. 144
Regulatory Gene Network for Specification of Mesoderm in the Xenopus Embryo p. 159
Gene Regulatory Network Controlling Dorsal-Ventral Territorial Specification in the Drosophila Embryo p. 166
Networks that Control Construction of Components of Adult Body Parts p. 175
Network Organization in the Specification of Pancreatic [beta]-Cells p. 176
Cell Fate Exclusion by microRNAs in a Gene Regulatory Controlling Terminal Differentiation in C. elegans Taste Network Neurons p. 180
Concluding Remarks p. 184
Gene Regulatory Networks: The Roots of Causality and Diversity in Animal Evolution p. 187
Evolutionary Implications of the Structure and Function of Gene Regulatory Networks p. 188
The Parts of Gene Regulatory Networks, and the Qualities of Evolutionary Change p. 188
Linnaean Framework for the Evolutionary Consequences of Alterations in Gene Regulatory Networks p. 195
Bilaterian Kernels, Predicted and Real p. 196
Caveats and a Caution p. 197
Regional Specification in the Bilaterian Nervous System p. 200
The Bilaterian Gut p. 212
A Possible Pan-Bilaterian Kernel Underlying Specification of the Heart Progenitor Field p. 218
Distribution of Kernels p. 221
Subphyletic Evolution of Bilaterian Body Plans: hox Genes as Sources of Labile Network Input/Output Switches p. 223
Diverse Functional Consequences of hox Gene Expression p. 223
Multiple Examples: Regional Repression and Installation of Patterning Output, and the Evolutionary Diversification of Body Parts p. 224
hox Gene Subnetworks and Spatial Evolution p. 233
Metazoan Origins and Gene Networks Before Kernels p. 235
"Deconstructing" Bilaterian Gene Regulatory Networks in Time p. 235
Concluding Reflection: The Principle of Animal Development and Evolution p. 239
References p. 241
Figure Citations p. 275
Index p. 279
The "Regulatory Genome" for Animal Development p. 1
The Framework p. 1
The Regulatory Apparatus Encoded in the DNA p. 3
Genomes, Genes, and Genomic "Space" p. 3
Overview of Regulatory Architecture p. 8
Gene Regulatory Networks p. 11
The Regulatory Demands of Development p. 16
Readout and Generation of Regulatory Information in Developmental Specification p. 16
Spatial Gene Expression p. 18
From Regional Specification to Terminal Differentiation p. 21
Evolution, Development, and the Regulatory Genome p. 27
cis-Regulatory Modules, and the Structure/Function Basis of Regulatory Logic p. 31
General Operating Principles p. 31
Modularity, A General Property of Genomic cis-Regulatory Control Units p. 33
Inside the cis-Regulatory Module: Logic Processing and Input/Output Relations p. 47
cis-Regulatory Logic Processors: Examples p. 48
Target Site Occupancy and Transcriptional Output p. 57
Generalization: The Combinatorial cis-Regulatory Logic Code p. 59
cis-Regulatory Design p. 61
Integration of Spatial Inputs at the cis-Regulatory Level p. 61
Repression and the Diversity of cis-Regulatory Design p. 68
cis-Regulatory Design and the Creation of Spatial Complexity in Development p. 73
Control by Sequence-Specific Interactions Among Distant cis-Regulatory Elements p. 78
Development and BTA Specificity p. 79
Control Functions of Sequence-Specific, Intra- and Intergenic Genomic Looping p. 80
Development as a Process of Regulatory State Specification p. 87
Developmental Processes of the Pregastrular Embryo p. 87
Vectorial Embryogeniss p. 88
Maternal Anisotropy and External Cues for Axial Polarity p. 90
Spatial Regulatory Complexity and Interblastomere Signaling p. 94
Territories p. 100
Comparative View of Embryonic Processes, and the Organization of the Underlying Gene Regulatory Networks p. 102
Shallow Gene Regulatory Networks of Type 1 Embryos p. 103
More Complex Forms of Embryonic Process p. 109
Regulatory State and Network Circuitry in Building Adult Body Parts p. 114
Steps in the Postembryonic Developmental Process p. 114
The Progenitor Field Concept p. 115
Subdivision of the Progenitor Field Regulatory State p. 121
Body Plan Development and the Organism p. 122
Gene Regulatory Networks for Development: What They Are, How They Work, and What They Mean p. 125
General Structural Properties of Developmental Gene Regulatory Networks p. 126
Overall Network Structure p. 127
Gene Regulatory Networks from Different Perspectives: Subcircuits to Process Diagrams p. 135
Qualitative Diversity of Network Components p. 136
Extensions p. 140
Gene Regulatory Networks for Embryonic Development p. 144
The Sea Urchin Endomesoderm Network p. 144
Regulatory Gene Network for Specification of Mesoderm in the Xenopus Embryo p. 159
Gene Regulatory Network Controlling Dorsal-Ventral Territorial Specification in the Drosophila Embryo p. 166
Networks that Control Construction of Components of Adult Body Parts p. 175
Network Organization in the Specification of Pancreatic [beta]-Cells p. 176
Cell Fate Exclusion by microRNAs in a Gene Regulatory Controlling Terminal Differentiation in C. elegans Taste Network Neurons p. 180
Concluding Remarks p. 184
Gene Regulatory Networks: The Roots of Causality and Diversity in Animal Evolution p. 187
Evolutionary Implications of the Structure and Function of Gene Regulatory Networks p. 188
The Parts of Gene Regulatory Networks, and the Qualities of Evolutionary Change p. 188
Linnaean Framework for the Evolutionary Consequences of Alterations in Gene Regulatory Networks p. 195
Bilaterian Kernels, Predicted and Real p. 196
Caveats and a Caution p. 197
Regional Specification in the Bilaterian Nervous System p. 200
The Bilaterian Gut p. 212
A Possible Pan-Bilaterian Kernel Underlying Specification of the Heart Progenitor Field p. 218
Distribution of Kernels p. 221
Subphyletic Evolution of Bilaterian Body Plans: hox Genes as Sources of Labile Network Input/Output Switches p. 223
Diverse Functional Consequences of hox Gene Expression p. 223
Multiple Examples: Regional Repression and Installation of Patterning Output, and the Evolutionary Diversification of Body Parts p. 224
hox Gene Subnetworks and Spatial Evolution p. 233
Metazoan Origins and Gene Networks Before Kernels p. 235
"Deconstructing" Bilaterian Gene Regulatory Networks in Time p. 235
Concluding Reflection: The Principle of Animal Development and Evolution p. 239
References p. 241
Figure Citations p. 275
Index p. 279
The regulatory genome : gene regulatory networks in development and evolution / New ed.
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