2. Enhancer Action: are there air-traffic controllers?
Many genes are pervasively expressed throughout development and exhibit changes of expression in a stage-specific manner. It is appreciated that different cis-regulatory modules (CRMs), also known as enhancers, act to control dynamic expression; however, not much is known about how enhancer order of action is regulated. Using the Drosophila embryo as a model system, we have the exceptional opportunity to investigate how enhancers support spatiotemporally-regulated gene expression during animal development. Current experiments focus on understanding how enhancer order of action is controlled. In particular, we are investigating whether promoter proximal elements work to balance enhancer input. This is important for regulating activation, for example, to control spatial outputs as well as levels of expression. The brinker gene locus is particularly well-suited to provide insight into the regulation of temporal gene expression. Our preliminary data show that the sequence just upstream of the brk minimal promoter contributes to sequential, coordinate action of CRMs controlling expression in the early embryo (see Dunipace et al., Dev Cell 2013). However, how this promoter proximal sequence as well as chromatin conformation supports timing of CRMs acting in series is not yet understood, and will be investigated. In addition, a necessary technical advance for analysis of dynamic developmental systems is analysis of chromatin conformation on a cell by cell basis, which will support studies of when and how particular CRMs interact with the promoter with temporal and spatial resolution. To this end, we are developing various technologies to acquire information about chromatin conformation and the Drosophila embryo is our test tube! We are also looking broadly at the regulation of gene expression over time and how enhancer action is regulated to effect change.