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Gene Regulatory Networks and the Evolution of Animal Body Plans Eric H. Davidson, Douglas H. Erwin Science 2002, 295:1669 (2002) National Academy of Sciences, April 5, 2005; 102 侯紹敏 李懿瑋 游竣評 郭嫚茜 張凱迪 中央大學 系統生物與生物資訊研究所 1 Outline • Development of the animal body plan • Different rate in the evolution • Developmental GRNs features and four components • How GRNs explain changes of the evolution • Summery 2 Body plan • blueprint • symmetry, # of body segments and # of limbs • tube-within-a-tube vs. sac-like • triploblasty http://users.tamuk.edu/kfjab02/Biology/Introzoology/b1313_ch16.htm 3 triploblasty Baer's laws for embryology: Two rules from four 1. The general characters of the group to which an embryo belongs appear in development earlier than the special characters. 2. The less general structural relations are formed after the more general, and so on, until the most specific appear. 4 Schematic representation of sea urchin embryo development P. Oliveri, E. H. Davidson, Curr. Opin. Genet. Dev. 14, 351(2004). 5 顯生宙 4700 ma 冥古代 Major diversification of life in the Cambrian Explosion. Many fossils Marinoan glaciations Possible "snowball Earth" period. Followed by Good fossils of multi-celled animals. oxygen levels in the atmosphere increased 元古宙 太古宙 630~8 50 ma http://en.wikipedia.org/wiki/Geologic_time_scale 6 Relationship Body plans dev Different combination of TF, cis-regulatory module Temporal , spacial GRN GRN structure is inherently hierarchical, because each phase of development has beginnings, middle stages, and progressively more fine-scale terminal processes. 7 Gene regulatory network Regulatory genes cis-regulatory modules linkages cis-regulatory modules: eg. enhancer, silencer , insulator > 300bp > 10 binding sites > 4 transcription factors 8 "Box-and-arrow" diagrams intercellular component transcription repess Known sequence P. Oliveri, E. H. Davidson, Curr. Opin. Genet. Dev. 14, 351(2004). 9 Sea urchin VS. Starfish Kingdom: Animalia Phylum: Echinodermata Class: Echinoidea Kingdom: Animalia Phylum: Echinodermata Class: Asteroidea 10 Kingdom biological classification From Wikipedia 11 Q1: why So little change in phylumand superphylum-level body plans since the Early Cambrian? Like Tetrapod, segmented. Q2: why Great changes have subsequently occurred within phyla and classes? 12 GRN Components • Kernels - inflexible, upstream • plug-ins – repeatedly coopted • Switch - I/O devices • gene batteries 13 Kernels • consist of regulatory genes • to specify the spatial domain • given developmental functions • particular form - recursive wiring • Interference with expression-> destroy kernel function altogether 14 switch plug-in plug-in kernel 2 3 4 switch Gene batteries 15 Echinoderms endoderm • a gene regulatory feedback loop • all except delta are regulatory genes • highly recursive • phase endoderm(yellow) mesoderm(gray) • surrounded by other network linkages that are not conserved EH Davidson and DH Erwin. Science 2002, 295:1669 (2002) 16 developmental processes for the heart • the linkages are also highly recursive. • eg. the nkx2.5, tbx, mef2c, and gata4 genes all receive inputs from multiple other genes of the kernel, as do the tin, doc, mid, pnr, and mef2c genes of the Drosophila network. EH Davidson and DH Erwin. Science 2002, 295:1669 (2002) 17 Additional examples • Anterior to posterior and midline to lateral specification of the nervous system • Eye field specification • Gut regionalization • Development of immune systems • Regionalization of the hindbrain and specification of neural crest 18 Plug-ins • Structurally conserved • used within and among species • not dedicated to formation of given body parts, providing inputs into regulatory apparatus • eg. affecting a confined repertoire of transcription factors, are used repeatedly, often acting as dominant spatial repressors in the absence of ligand and as facilitators of spatially confined expression in its presence. 19 Hedgehog signal • Wnt • Transforming growth factorB • Fibroblast growth factor • Hedgehog • Notch • Epidermal growth factor • Flexible • Homologous processes in related animals • Evolutionarily very labile K. M. Cadigan, R. Nusse, Genes Dev. 11, 3286 (1997). 20 Gene batteries • Only deployed at the end of this process • structural genes :protein-coding genes • the products of which execute cell type–specific functions • Differentiation gene batteries display inherent evolutionary lability and undergo continuous renovation 21 Gene batteries properties Outputs terminate the network at the periphery of developmental GRNs • Control the progressive formation of spatial patterns of gene expression 22 switch • may be regulating other network subcircuits • appear to be responsible for many kinds of evolutionary change in developmental process Eg. Cell cycle control hox gene ->direct repressive on expression of wing-patterning genes -> morphology 23 Predicted Evolutionary Consequences of Changes in GRN Architecture Change in them is prohibited Once GRNs kernels assembled since Cambrian ,they could not be disassembled! The most frequent and least constrained EH Davidson and DH Erwin. Science 2002, 295:1669 (2002) 24 • Micro evolutionary thinking-> Temporally homogeneous way intersects with mechanisms of GRN change • Comparative molecular-> the evolutionary point of origin 25 • GRNs of subsequent adaptational change is forced to lower since Cambrian. • Early assembly of kernels, plug-in and switch, AND piecemeal alteration of gene batteries provide evolution. • The conserved kernels of extant developmental GRNs is the answers 26 Summery cis-regulatory DNAs execute The program for development regulate transcription factors components of cell signaling pathways classes of GRN componen • • • • kernels plug-ins Switch gene batteries 27 References • M. Levine, E. H. Davidson, Proc. Natl. Acad. Sci. U.S.A.102, 4936 (2005). • P. Oliveri, E. H. Davidson, Curr. Opin. Genet. Dev. 14, 351(2004). • http://strc.herts.ac.uk/bio/maria/Projects.htm • W. J. R. Longabaugh, E. H. Davidson, H. Bolouri, Dev.Biol. 283, 1 (2005). 28 • Thank you!! 29