Berkeley Drosophila Transcription Network Project: 3D Blastoderm Gene Expression Atlas.
1) Life Sciences and Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA.
2) Computer Science Division, University of California, Berkeley, CA.
3) Institute for Data Analysis and Visualization, University of California, Davis, CA.
4) Computer Science Department, University of Kaiserslautern, Germany.
The Berkeley Drosophila Transcription Network Project (bdtnp.lbl.gov) is conducting a system-wide analysis of the transcription network in the early Drosophila embryo. As part of this multidisciplinary effort, novel imaging, image analysis, and visualization methods have been developed to construct the first three-dimensional (3D) atlas of gene expression and morphology in an embryo at cellular resolution. Our aim is to quantify the relative expression of 1,000 genes in wild type embryos and up to 200 genes in a series of mutant embryos, and to map these results onto representatives of "stereotypical" embryos. Multiple-color in-situ-hybridizations are used to fluorescently label gene products of interest and total DNA is counter-stained. High resolution, multi-channel, 3D images are acquired of entire embryos using two-photon excitation. Individual nuclei are isolated from the DNA-stained images using novel, automated segmentation techniques and the associated cellular extent of each nucleus is then estimated using morphological cues. The resulting segmentation mask is used to quantify the relative gene expression from the other channels and produce tables of relative gene expression per nuclei, "pointcloud" data. Novel techniques have been developed to pair-wise align multiple images into a "stereotypical embryo" and create exquisite quantitative visualizations of the data in 3D. Currently we have acquired data for 20 gap and pair-rule genes at multiple time-point spanning stages 4 and 5. Our methods have uncovered complex 3D nuclear movements prior to gastrulation that help determine the dynamic changes in gene expression patterns. It is our hope that this gene expression atlas will serve as a quantitative reference to identify transcription factor target genes and model the dynamics of the gene regulatory network and morphogenesis.
Last modified March 9, 2006.