nemhauser lab
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Analyzing how hormones trigger global changes in cellular programs

Summary: Many proteins required for normal photomorphogenesis change which genes are on and off. We and others have looked at the levels of expression of all genes in the genome following hormone treatment to try to understand which genes are shared by different signals. We are now implementing a new method to identify which regions of DNA are bound by proteins when hormones are present.

What genes are on or off? In addition to providing clues about specific signaling pathways, transcript profiling provides a quantitative phenotype to probe the nature of interactions between pathways. This type of analysis has revealed that hormones are tightly interconnected—with each hormone triggering a domino effect on other hormone biosynthetic and signaling pathways.

What pieces of DNA are important? The orchestrated binding of transcriptional activators and repressors to DNA sequences defines the regulatory program of eukaryotic genomes. The Arabidopsis community has assembled a substantial collection of transcriptional profiles documenting widespread genome reprogramming following exposure to a number of environmental cues. These previous studies tell us which genes may be important for plant responses, but we know very little about the regulatory regions (and the proteins bound to them) orchestrating these global transitions. The Nemhauser Lab has recently begun a collaboration with the labs of John Stamatoyannopoulos and Christine Queitsch in the UW Genome Sciences Department. Together, we are applying a high-throughput approach called digital DNaseI footprinting to delineate regulatory DNA across the Arabidopsis genome. Using this approach, we will learn the precise DNA elements associated with environmentally-triggered genome transitions.