Grace Yuh Chwen Lee

Organisms have evolved ways to “mark” TE sequences with repressive epigenetic marks, which reduce the ability of TEs to move and to multiply. However, as a side effect, the repressive epigenetic marks at TEs could “spread” to neighboring genes. I found this phenomenon (“epigenetic effects of TEs”) is highly prevalent in Drosophila genomes, can interfere with gene function, and is strongly selected against by natural selection. I am investigating the variation of TE's epigenetic effects within and between species, and identifying genetic factors responsible for such variation, with the goal of understanding the role of TE's epigenetic effects in the evolution of both TEs and host genomes.

While TEs have been found in virtually all eukaryotic genomes surveyed, there is substantial variation in their abundance, composition, and frequency spectrum within and between species. I investigate how the evolutionary dynamics of TEs is influenced by selection against various harmful effects of TEs, the replication mechanism of TEs, and the evolutionary history of hosts. I use empirical population genomics and modeling to address this question, with special focus on the condition leading to “stable containment” of TEs in host populations.

I led in the first comprehensive study of coding sequence evolution in the Drosophila Population Genomics Project (DPGP). Through that and other parallele projects, I revealed that not only external environmental factors, but also internal genetic processes significantly influence polymorphism within and divergence between spciess. I am continuingly investigating how various fundamental genetic and molecular processes, as well as the antagonistic interactions between repetitive sequences and host molecular machineries, influence gene evolution.