Evolutionary Epigenetics lab

transposable elements, population genetics, epigenomics, Drosophila

About us

The Lee lab is part of the Ecology and Evolutionary Biology at the University of California, Irvine.

We are interested in how fundamental internal genetic processes impact genome evolution. In particular, we focus on the evolution of a widespread genomic parasite, “transposable elements” (TEs), who can copy themselves and move to new genomic locations. We study how TEs are harmful to their hosts and how selection against these harmful effects influences TE’s own evolutionary dynamics and, in return, genome function and evolution. We use Drosophila (fruit flies hovering over fruits!!) as a model system, and combine approaches of population genetics, genomics, epigenetics, and chromosome biology.

In addition to TEs, we study the evolution of non-repetitive sequences, in particular protein coding sequences. We address how various internal cellular and molecular processes, such as recombination, mutation, and 3D organization of the genome, as well as the antagonistic interaction with genetic parasites may shape genome evolution.

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, which, we strikingly found, can lead to changes in the 3D nuclear structure of the genome. 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. We are investigating the variation of TE's epigenetic effects within and between species and the causes for such variation. Ultimately, we want to understand 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. We are investigating 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. We combine both empirical population genomics and theoretical modeling to address these questions.

Evolutionary genomics of coding sequences

We have a continuing interest in understanding the evolution of protein coding genes. Our previous work demonstrates that not only external environmental factors, but also internal genetic processes influence the variation of genic sequences within and between species. We are investigating how fundamental molecular and cellular processes, as well as the antagonistic interactions between repetitive sequences (including TEs!) and host molecular machineries, influence gene evolution.

Current Members

Grace Yuh Chwen Lee - PI

Grace received her Ph.D. from UC Davis with Charles Langley on population genetics. She did postdocs with Manyuan Long at the University of Chicago on evolutionary genetics and with Gary Karpen at the Lawrence Berkeley National Lab on epigenetics and chromosome biology. Grace joined the faculty at the UC Irvine as an Assistant Professor of Ecology and Evolutionary Biology in July 2019.

Grace has been a big fan of transposable elements, and she loves the beauty of tiny fruit flies. When not playing with flies or computers, Grace is usually going for a walk with Purin (named after this character), a 12-year young Yorkie rescue (senior dogs rock!!). She is also an avid classical music lover and enjoys going to concerts.

Yuheng Huang - postdoc

Yuheng did his Ph.D. at U. Toronto with Aneil Agrawal, where he used experimental fly populations to study the effects of varying environments on genetic variation, adaptability, and transcriptomic plasticity. He did a postdoc at UW-Madison with John Pool, where he studied the genomic and transcriptomic basis of adaptation to cold environments in natural fly populations. Currently, Yuheng is studying the interplay between epigenetics and the evolution of gene regulation.

Fruit fly is Yuheng's favorite model organism. Its easiness to keep in the lab, short generation time, and a wide range of genetic resources allow him to experimentally study interesting evolutionary genetic questions. Outside the lab, Yuheng enjoys reading, jogging, and playing table tennis.

Jasmine Osei-Enin - technician

Jasmine was a McNair Scholar with a B.S. degree in Evolution, Ecology, and Biodiversity from UC Davis. She worked as an undergraduate researcher in Michael Turelli's lab, studying the distribution and phenotypic effects of wolbachia in various Drosophila species. Jasmine loves to do yoga, listen to music, and spend time with friends.


Join the lab

We are actively looking for enthusiastic postdocs and students to join us!

Postdocs - If you are looking for a postdoc and find that our research interests align, please send Grace your CV and a one-page description of your research interest and career goal.

Graduate students - For prospective graduate students, we are part of the graduate program of the Department of Ecology and Evolutionary Biology, the Mathematical, Computational, and Systems Biology (MCSB) Gateway program, and the Genetics, Epigenetics, and Genomics (GEG) graduate program. If you are interested in joinning the lab as a graduate student, please send Grace your CV and reserach interest, so we can discuss which graduate program may be the best to apply to.

Undergraduate students - We welcome dedicated and motivated undergraduate students to join us. Please send Grace a short description of why you would like to join the lab, your backgroud in science (biology/math/computer science etc), and you generally as a person.


  • Choi, J.C. and Y.C.G. Lee
    Double-edged sword: the evolutionary consequences of the epigenetic silencing of transposable elements.
    in review in PLoS Genetics
  • Lee, Y.C.G., Y. Ogiyama, D. Acevedo, N.C. Martins, B.J. Beliveau, C.T. Wu, G. Cavalli, and G.H. Karpen. (2020)
    Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2/3 islands located in euchromatic genome.
    PLoS Genetics 16 (3), e1008673. link
  • Mills, W.K., Y.C.G. Lee, A.M. Kochendoerfer, E.M. Dunleavy, and G.H. Karpen. (2019)
    RNA transcribed from heterochromatic simple-tandem repeats are required for male fertility and histone-protamine exchange in Drosophila melanogaster.
    eLife 8. link
  • Lee, Y.C.G., I.M. Ventura, G.R. Rice, D.Y. Chen, and M. Long. (2019)
    Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes.
    Molecular Biology and Evolution 36 (10), 2212-2226. link
  • Lee, Y.C.G. and M.T. Levine. (2017)
    Germline genome protection on an evolutionary treadmill.
    Developmental Cell 43(1): 1-3. link
  • Lee, Y.C.G. and G.H. Karpen. (2017)
    Pervasive epigenetic effects of euchromatic transposable elements that shape their own evolution.
    eLife 6:e25762. recommended by F1000 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
  • 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


5323 McGaugh Hall, UC Irvine
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