Over the years, we have become increasingly interested in developing both genetic and biochemical approaches that can be applied in vivo to study transcription and its regulation. Our primary model system is the highly-inducible heat shock (HS) genes in Drosophila. (Why study heat shock genes?) We also use stem cells and yeast for various assays.
Studying transcription regulation requires highly sensitive tools for “imaging” specific macromolecular interactions. Determining the associations of transcription factors along a promoter and gene during the kinetics of gene activation can limit the possible models for the roles of these factors. We examine interactions both optically, using microscopy to actually see where factors are, and molecularly, using biochemical techniques.
Our imaging can be dramatically enhanced by additional strategies that lead to the disruption of specific factors or their macromolecular interactions, and then re-examining (re-imaging) other factors involved in the process to observe the changes.
Disruption can be achieved in several ways, each with specific advantages and drawbacks. Some are easy and generally applied, such as RNAi, but may not be good at sorting primary from secondary effects. Others are harder to implement, but are better at rigorously identifying the direct effects of a factor, such as RNA aptamers.