Genomic Control Process: Development and Evolution

http://dx.doi.org/10.1016/B978-0-12-404729-7.00002-2 Copyright © 2015 Eric H. Davidson and Isabelle S. Peter. Published by Elsevier Inc. All rights reserved. 1. Introductory Overview of Developmental GRNs 42 1.1 GRN function and how GRNs are encoded in the genome 42 1.2 GRN hierarchy and modular organization 43 1.3 Models of GRN topology 44 2. Boolean Spatial Output 45 3. Regulatory States 48 4. Regulation in Cis 48 4.1 CRM genomics 48 4.2 CRM logic functions 49 4.3 Flexibility and constraint in CRM sequence 50 5. Module Choice 54 5.1 General looping mechanisms 55 5.2 Specificity of looping 57 6. Transcriptional Dynamics 58 6.1 Transcriptional initiation and the life and death of mRNA 58 6.2 Productive cis-regulatory occupancy by transcription factors in the nucleus 62 6.3 Regulatory cascade dynamics 67 7. Historical Origins and Antecedents of GRN Theory 70 7.1 Organism-wide genomic regulatory system required for development 71 7.2 Combinatorial transcriptional regulation of spatial gene expression 71 7.3 Hierarchical structure of GRNs 72