John Lis

Research Focus

The Lis Lab develops and uses a variety of strategies to study the structure of promoters and genes and the mechanisms of their regulation in living cells. Our main model system has been the heat shock genes. These genes can undergo a 200-fold activation of transcription in response to small change in temperature and other cellular stresses. Over the years, we have developed genetic, optical and biochemical approaches that can be applied to study gene transcription and regulation with high precision and specificity in vivo. These include approaches that view the underlying mechanisms at the molecular level and in their native cellular environment. While our studies in the past were focused on a few genes, new genome-wide methods, several which we have developed, allow the interrogation of the entire genome – often with higher precision and sensitivity than our older focused gene studies. The genome-wide approaches are allowing the generality of hypotheses to be tested, and they are providing massive data for generating new hypotheses of how genes are regulated.
We test our proposed molecular mechanisms by examining the consequences of targeted disruption of key protein factors or factor activities. This disruption of factors can be achieved by several strategies. Some strategies are easy and generally applied, such as RNAi, but are not effective at sorting primary from secondary effects. Others can be harder to implement, but are better at rigorously identifying the direct effects of a factor. We frequently use highly-specific small molecule inhibitors of the enzymes involved in transcription and regulation, when such molecules are available. Additionally, we have invested heavily in developing efficient selection methods for RNA aptamers that bind specific factors. RNA aptamers are of particular interest to us as they provide alternatives to small-molecular-weight "drugs" and can be selected in vitro from large combinatorial sequence pool for their affinity to a target protein. Next generation sequencing and use of our multiplex devices in selections have dramatically increased the rate production of RNA aptamers that bind target molecules with high affinity and specificity. These RNA aptamers are large enough to bind tightly to macromolecular surfaces and disrupt/inhibit interactions of a targeted macromolecule. Additionally, these aptamers can be targeted with precision by expressing the RNAs in cell under the control of specific promoters, allowing modulatation or perturbation of molecular interactions with high temporal and spatial precision in tissue culture cells or animals.