Quantitative 3D Analysis of Expression Patterns Driven by cis-Regulatory Modules.
1) Life Sciences and Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA.
2) Department of Computer Science, University of California, Irvine, CA.
3) Computer Science Division, University of California, Berkeley, CA.
The Berkeley Drosophila Transcription Network Project (http://bdtnp.lbl.gov/) has recently developed methods for collecting cellular resolution quantitative expression data in whole blastoderm embryos in a computationally analyzable format. Baseline data has been collected on the mRNA and/or protein expression patterns of over 100 genes as part of a larger effort to predict transcriptional output from genomic DNA sequences. However, the complete pattern of each gene's expression is built up by the combined action of multiple cis-Regulatory Modules (CRMs). To investigate how complete patterns are established, we are quantitating the expression driven by individual CRMs. This is critical, as previous transgenic promoter experiments have been limited by lack of quantitative resolution and computational analysis. We find that a number of CRMs drive patterns of transcription that differ from those of the corresponding pattern elements of the intact gene in native context, e.g., by having less distinct borders at expression boundaries. Thus our quantitated CRM expression patterns will provide a more precise basis for modeling transcriptional output from specific DNA sequences and allow analysis of how sequences outside of individual CRMs help refine the output of the CRM. In addition, we are comparing transcript levels in nuclei vs cytoplasm to characterize the expression dynamics of different CRMs.
Last modified March 27, 2008.