John T. Lis

Biosketch

My lab develops and uses a variety of strategies to probe the structure of promoters and genes and the regulation of their activities in living cells. We have studied the factors and mechanisms that drive transcription and its regulation for decades. While our primary model system has been the highly-inducible heat shock (HS) genes in Drosophila, we have over the past several years become deeply committed to developing and using genome-wide assays in Drosophila and mammalian cell lines to measure, often with base pair precision, the process of transcription and the interaction of regulatory transcription factors. The challenging problem being addressed in this proposal is to examine the functional interactions of human regulatory elements and promoters that is so essential to understanding how genomes are regulated. We will address this important regulatory problem with the powerful high-throughput methods developed by my collaborator, Dr. Yaiyuan Yu and our own novel variation of the powerful published STARR-seq protocol by the Stark Lab. These highthroughput methods will identify key enhancers as well as variants and mutants with strong phenotypes that will then be tested in a rigorous manner using transgenic genetic lines where variant and mutated versions are at there native locus. The molecular interplays of the enhancers and selected variants/mutants will be explored with a battery of highly sensitive, and high resolution genome approaches.

Research Interests

My research interests concentrate on promoters and genes and their mechanisms of regulation. For many years, my laboratory has focused on a few highly-inducible heat shock (HS) genes in drosophila as models, and these studies led to the discovery of a key transcriptional regulatory step of RNA polymerase II promoter-proximal pausing. More recently, using genome-wide assays that we developed in both drosophila and mammals, we have shown this regulation is general. To examine the molecular mechanics of this regulation in living cells, we employed existing technology and developed new approaches designed to inhibit the activities or interactions of specific transcription factors. Our current efforts examine the consequences of these specific inhibitions in vivo using high-resolution and genome-wide assays. One important strategy we developed uses RNA aptamers that are selected to bind and inhibit specific target proteins. We have improved the efficiency of RNA aptamer selections and are expressing aptamers against critical transcription factors in cells and animals. The rapid expression of these aptamers in vivo when coupled with our high resolution, genome-wide assays is revealing novel mechanistic insights to molecular mechanisms of transcription regulation. Our plan is to expand this approach to examine the role of many key transcription factors.