analysis of gap gene regulation in a 3d organism-scale model of the drosophila melanogaster embryo分析差距在3 d organism-scale基因调控模型的黑腹果蝇胚胎.pdfVIP

Analysis of Gap Gene Regulation in a 3D Organism-Scale Model of the Drosophila melanogaster Embryo 1 1 2 3 4 James B. Hengenius , Michael Gribskov , Ann E. Rundell , Charless C. Fowlkes , David M. Umulis * 1 Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America, 2 Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America, 3 Department of Computer Science, University of California Irvine, Irvine, California, United States of America, 4 Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, United States of America Abstract The axial bodyplan of Drosophila melanogaster is determined during a process called morphogenesis. Shortly after fertilization, maternal bicoid mRNA is translated into Bicoid (Bcd). This protein establishes a spatially graded morphogen distribution along the anterior-posterior (AP) axis of the embryo. Bcd initiates AP axis determination by triggering ex- pression of gap genes that subsequently regulate each other’s expression to form a precisely controlled spatial distribution of gene products. Reaction-diffusion models of gap gene expression on a 1D domain have previously been used to infer complex genetic regulatory network (GRN) interactions by optimizing model parameters with respect to 1D gap gene expression data. Here we construct a finite element reaction-diffusion model with a realistic 3D geometry fit to full 3D gap gene expression data. Though gap gene products exhibit dorsal-ventral asymmetries, we discover that previously inferred gap GRNs yield qualitatively correct AP distributions