3-Dimensional quantitative analysis of gene expression in multiple Drosophila species.
1) Molecular and Cellular Biology, University of California, Berkeley, CA.
2) Life Sciences and Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA.
3) Computer Science Division, University of California, Berkeley, CA.
Understanding how transcriptional regulatory sequences evolve requires us to link changes in sequence with changes in function. The Berkeley Drosophila Transcription Network Project (BDTNP http://bdtnp.lbl.gov) is characterizing the transcriptional regulatory elements that control early development in, Drosophila melanogaster and quantitatively describing their function, i.e ., the patterns in which the corresponding genes are expressed. A novel set of computational tools converts confocal images of fluorescently stained blastoderm embryos into a composite 3D map where averaged expression patterns for many genes are present in the same cellular resolution morphological framework. We are now applying these high-resolution imaging methods to a closely related Drosophila species, D. pseudoobscura. We are determining the expression patterns of key transcriptional regulators and a subset of their targets, including genes adjacent to potential regulatory regions with interesting binding site dynamics, such as overall changes in composition and lineage specific gains and losses. Because we can detect subtle quantitative and spatial changes in expression patterns, this imaging approach is particularly well suited to discovering whether even small sequence changes alter gene regulation. By including many genes in our models, we can interpret these changes in the context of the regulatory network as a whole. Computational analysis of the spatial relationship between gene expression patterns can glean candidate regulatory relationships and allow us to hunt for regulatory novelty at the level of transcriptional network architecture. This type of detailed functional characterization of the output of regulatory elements will allow us to interpret the abundant regulatory sequence variation across the recently sequenced Drosophila species.
Last modified March 27, 2008.