Genomic control process : development and evolution / Isabelle S. Peter, Eric H. Davidson, California Institute of Technology, Pasadena, CA. -- Amsterdam : Academic Press, [2015]. – (58.215/P478)

Contents

Preface

Chapter 1: The Genome in Development

1. Views of Development

2. Levels of Control of Gene Expression: Transcriptional Regulation

3. Levels of Control of Gene Expression: Noncoding RNAs

4. Levels of Control of Gene Expression: Histone Modifications

5. The Regulatory Genome

Chapter 2: Gene Regulatory Networks

1. Introductory Overview of Developmental GRNs

2. Boolean Spatial Output

3. Regulatory States

4. Regulation in Cis

5. Module Choice

6. Transcriptional Dynamics

7. Historical Origins and Antecedents of GRN Theory

Chapter 3: Gen0mic Strategies for Embryonic Development  79

1. Common Principles of Embryonic Development

2. Phylogenetic Framework

3. Genomic Strategies of Control in Mode 1 Embryonic Processes

4. Genomic Strategies of Control in Mode 2 Embryonic Processes

5. Global Aspects of A/P Spatial Regulatory Patterning in the Syncytial Drosophila Blastoderm

Chapter 4: Genomic Control Processes in Adult Body Part Formation

1.  Common Principles of Body Part Formation

2.  Limbs in Amniotes

3.  Fly Legs

4.  Establishment of Spatial Regulatory States in Early Development of Fly and Mammalian Brains

5. The Vertebrate Heart

6. Spatial Regulatory State Subdivision in and Around the Drosophila Ocellus

7. The Vertebrate Cut

Chapter 5: Genomic Strategies for Terminal Cell Fate Specification

1.  Circumstances of Terminal Cell Fate Specification

2.  Combinatorial Cis-Regulatory Definition of Differentiation Gene Batteries

3.  Cell Type Specification in Multipotential Embryonic Precursors

4.  A Comment on Stem Cells in Postembryonic Life

5.  Modular Call-Up of Given Specification Processes in Multiple Developmental Contexts

Chapter 6: On the Modeling of Developmental Gene Regulatory Networks

1. Topological Network Models

2. ODE Models of Circuit Dynamics

3. Boolean Models of Network Logic

4. Conclusions

Chapter 7: Evolution of Bilaterian Animals: Processes of Change and Stasis in Hierarchical Developmental Gene Regulatory Networks     327

1.  Introduction: Evolution by Genomic Change at Different Levels of GRN Hierarchy

2.  Evolution of the Body Plan by Co-Optive Alteration of GRN Structure

3.  GRN Stasis and Phylogeny

4.  Trans-Phyletic Conservation of Cell Type-Specific Regulatory States

5.  Bilaterian Evolution

Gene Index

Subject Index