Beckman Fellow 2016-17

Thomas Kuhlman


Real Time Transposable Element Activity in Individual Live Cells

Professor Kuhlman’s laboratory uses the tools and techniques of physics to explore the molecular basis of mutation and evolution, using specially constructed fluorescent reporters to watch genome instabilities occur in real time and in living cells. His research team quantifies the statistics by which mutations and other genome reorganization arise, the influence of the environment on these statistics, and the effects of genome dynamics on the growth rate of the organism. In service of this project, Professor Kuhlman’s lab uses and develops state-of-the-art imaging, molecular and microbiological techniques, and microfluidics.

The genomes of all organisms contain transposable elements (TEs): parasitic genetic elements capable of self-catalyzed copying, proliferation, and integration into the host genome. As a result of this activity, the host genome can be significantly altered and disrupted: approximately 50% of the human genome is made up of TEs and their remnants as “junk DNA,” and their activity is the direct causative agent of many diseases. However, despite their importance and ubiquity, relatively little is known about the statistics and rates of transposition, and the distribution of effects on the host. To resolve this fundamental gap in the understanding of a basic building block of all genomes, Professor Kuhlman’s lab has developed a synthetic TE whose activity results in the expression of fluorescent reporter proteins. As a consequence, the dynamics of TE propagation within living cells can be studied in spatially-resolved detail and in real time, to quantitatively characterize their contribution to and effects upon the health of the organism, and to investigate their interplay with other processes contributing to genome plasticity and their propagation throughout populations. The method is extensible to all types of TEs and cell types, and this real-time approach will potentially revolutionize our understanding of the dynamics of transposable elements, the evolution of genomes and “junk DNA,” and our understanding of human disease caused by transposable elements.