Grace YC Lee

Grace Yuh Chwen Lee

Evolutionary geneticist, Drosophilist, music lover, and yorkie fanatic.

About Me

I am an evolutionary geneticist, studying the evolutionary forces shaping genomic variation within and between species. I am currently an NIH K99 postdoctoral fellow in Gary Karpen’s lab at Lawrence Berkeley National Laboratory and UC Berkeley. Previsouly, I was a postdoctoral fellow at the University of Chicago with Manyuan Long. I recieved my Ph.D. from UC Davis with Charles Langley.

I am especially interested in how fundamental internal genetic processes impact genome evolution. My research focuses on the evolution of a widespread genomic parasite, “transposable elements” (TEs), who can copy themselves and move to new genomic locations. I study how TEs are harmful to their hosts and how selection against these harmful effects influence TE’s own evolutionary dynamics and, more broadly, genome evolution. I use Drosophila (fruit flies hovering over fruits!!) as a model system, and combine global analyses (population genomics, functional genomics, modeling) with functional studies (experimental genetics, cell biology).

In addition to TEs, I also study the evolution of non-repetitive sequences, in particular protein coding sequences. I address how various internal genetic processes, such as recombination, organization of genetic elements, mutation processes, and the antagonistic interaction with genetic parasites may shape gene evolution.

When not playing with flies or computers, I am usually going for a walk with Purin, a ten-year young Yorkie who we recently adopted. I am also an avid classical music lover and have been enjoying concerts from highly diverse music groups in the Bay area.

Epigenetic effects of transposable elements

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.

Population genomics of transposable elements

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.

Evolutionary genomics of coding sequences

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.

Experience

2015- NIH K99 Postdocotoral Fellow
Lawrence Berkeley National Lab & University of California, Berkeley
advisor: Gary Karpen
2012-2015 NIH NRSA Postdocotral Fellow
University of Chicago
advisor: Manyuan Long
2012 Ph.D. in Population Genetics
University of California, Davis
advisor: Charles Langley
2006 B.S. in Life Sciences (Zoology emphasis)
National Taiwan University
reserach advisor: Alex Hon-Tsen Yu

Publications

  • Lee, Y.C.G. and G.H. Karpen. (2017)
    Pervasive epigenetic effects of euchromatic transposable elements that shape their own evolution.
    eLife 6:e25762. link
  • Lee, Y.C.G., Q. Yang, W. Chi, W. Du, S.A. Turkson, C. Kemkemer, Z.Z. Zheng, X. Zhuang, and M. Long. (2017)
    Genetic architecture of adult foraging behavior that is essential for the survival of Drosophila melanogaster.
    Genome Biology and Evolution 9 (5): 1357-1369. link
  • Turissini, D.A., A.A. Comeault, G. Liu, Y.C.G. Lee, and D.R. Matute. (2017)
    Drosophila hybrids have troubles finding food. Evolution 71-4:960-973. link
  • Lee, Y.C.G., C. Leek, and M.T. Levine. (2017)
    Recurrent innovation at genes required for telomere integrity in Drosophila. Molecular Biology and Evolution 34 (2): 467-482. link
  • Lee, Y.C.G. (2015)
    The role of piRNA-mediated epigenetic silencing in the population dynamics of transposable elements in Drosophila melanogaster. PLoS Genetics 11(6): e1005269. link
  • Lee, Y.C.G., C.H. Langley and D.J. Begun (2014)
    Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster. Molecular Biology and Evolution 31(4): 804-816. link
  • Lee, Y.C.G.* and H.H. Chang* (2013)
    The evolution and functional significance of nested gene structures in Drosophila melanogaster. Genome Biology and Evolution 5(10):1978-1985. link
  • Lee, Y.C.G. and C.H. Langley (2012)
    Long-term and short-term evolutionary impacts of transposable elements on Drosophila. Genetics 192(4):1411-32. Issue Highlight. link
  • Langley, C.H., K. Steven, C.M. Cardeno, Y.C.G. Lee, D.R. Schrider, J.E. Pool, S.A. Langley, C. Suarez, R. Detig-Corbet, B. Kolaczkowski, S. Fang, P.M. Nista, A.K. Holloway, A.D. Kern, C.N. Dewey, Y.S. Song, M.W. Hahn and D.J. Begun (2012)
    Genomic variation in natural populations of Drosophila melanogaster. Genetics 192(2):533-98. Issue Highlight. link
    Conducted the gene-based population and evolutionary genomic analysis. Authored a substantial proportion of the manuscript.
  • Levine, M.T., C. McCoy, D. Vermaak, Y.C.G. Lee, M.A. Hiatt, F.A. Matsen and H.S. Malik (2012)
    Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family. PLoS Genetics 8(6): e1002729. link
  • Lee, Y.C.G.* and J.A. Reinhardt* (2012)
    Widespread polymorphism in the positions of stop codons in Drosophila melanogaster. Genome Biology and Evolution 4(4):533-49. link
  • Lee, Y.C.G. and C.H. Langley (2010)
    Transposable elements in natural populations of Drosophila melanogaster. Philosophical Transactions of the Royal Society B 365: 1219-1228. link
*equal contribution

Contact

grylee
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