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Karpen Lab

Research Interest

The Karpen Lab researches four areas related to chromosome structure and function in higher eukaryotes, with a special interest in epigenomic regulation: 1) centromeric chromatin structure and propagation, 2) spatial and temporal regulation of DNA repair in heterochromatin, 3) genome-wide distributions and functions of histone modifications and chromosomal proteins (as part of the Model Organism Encyclopedia of DNA Elements project, or modENCODE), and 4) epigenomic regulation of the response to low dose radiation.

We are using a combination of genetic, genomic, biochemical and cell biological approaches to address these fundamental questions. The fly Drosophila melanogaster is our primary experimental system, but we are also exploring the relevance of our findings to other organisms, including humans. Defects in normal chromosome inheritance are involved in the etiology of cancer and birth defects, and increased knowledge of chromosomal mechanisms and regulatory molecules are likely to lead to tools for the diagnosis and treatment of human diseases.

Our investigations of how repeated DNAs located in a special domain called heterochromatin are repaired after damage have revealed dramatic responses to radiation-specifically visible expansion of the heterochromatin domain, and relocalization of repair foci outside the domain. Early steps in recombination repair (e.g. resection) occur within the heterochromatin domain, whereas later steps (e.g. strand invasion) are delayed until foci relocalize outside the domain. We propose that the unusual spatial and temporal regulation of recombination repair in heterochromatin helps maintain genome stability by avoiding exchange with undamaged repeats that result in translocations and chromosome loss.


atrip stills image

3D reconstruction of time-lapse analysis of movement of irradiation-induced repair foci (ATRIP, colors) outside the heterochromatin domain (HP1, grey). Arrowheads indicate time (white numbers) when similarly colored foci have moved to the periphery of the HP1 domain.


Selected Publications

Riddle, N.C., Minoda, A., Kharchenko, P.V., Alekseyenko, A.A., Schwartz, Y.B., Tolstorukov, M.Y., Gorchakov, A.A., Kennedy, C., Linder-Basso, D., Jaffe, J.D., Shanower, G., Kuroda, M.I., Pirrotta, V., Park, P.J., Elgin, S.C.R., Karpen, G.H. (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Research 21(2):147-63.

Kharchenko, P.V., Alekseyenko, A.A., Schwartz, Y.B., Minoda, A., Riddle, N.C., Ernst, J., Sabo, P.J., Larschan, E., Gorchakov, A.A., Gu, T., Linder-Basso, D., Plachetka, A., Shanower, G., Tolstorukov, M.Y., Luquette, L.J., Xi, R., Jung, Y.L., Park, R., Bishop, E.P., Canfield, T.P., Sandstrom, R., Thurman, R.E.,MacAlpine, D.M., Stamatoyannopoulos, J., Kellis, M., Elgin,S.C.R., Kuroda, M.I., Pirrotta, V., Karpen, G.H., Park, P.J. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471(7339):480-5.

modENCODE Consortium et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 24;330(6012):1787-97.

Williamson, A., Wickliffe, K.E., Mellone, Barbara G., Song, L., Karpen, G.H., Rape, M. (2009) Identification of a physiological E2 module for the human anaphase-promoting complex. PNAS 106, 18213-18218.

Peng, J. and Karpen, G.H. (2009) Heterochromatic genome stability requires regulators of histone H3 K9 methylation. PLoS Genetics 5(3): p. e1000435.

Erhardt, S., Mellone, B., Betts, C.M., Zhang, W., Karpen, G.H. and Straight, A.F. (2008). Genome-wide analysis reveals a cell-cycle-dependent mechanism controlling centromere propagation. JCB 183, 805-818.

Smith, C.D., Shu, S-Q., Mungall, C.J., and Karpen, G.H. (2007). The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science 316, 1586-1591. (PMC 2819280).

Hoskins, R.A, Carlson, J.W.*, Kennedy, C., Acevedo, D., Evans-Holm, M., Frise, E., Wan, K.H., Park, S.,Villasante, A., Mendez, M., Rossi, F., Dimitri, P., Karpen, G.H., and Celniker, S.E. (2007). Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316, 1625-1628.

Peng, J. and Karpen, G.H. (2007). H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nature Cell Biology 9(1), 25-35.

Heun, P., Erhardt, S., Blower, M.D., Weiss, S., Skora, A.D., and Karpen, G.H. (2006) Mislocalization of the Drosophila centromere-specific histone CID promotes formation of functional ectopic kinetochores. Developmental Cell 10(3), 303-15.

Blower, M.D., Sullivan, B.A., and Karpen, G.H. (2002). Conserved organization of centromeric chromatin in flies and humans. Developmental Cell 2, 319-330.



Gary Karpen

Senior Scientist &
Division Director/
Life Sciences Division

Adjunct Professor, UC Berkeley, Dept. of Molecular and Cell Biology

Genome Dynamics

Berkeley Lab
One Cyclotron Road
Mailstop: 977
Berkeley, CA 94720
Tel: (510) 495-2438
Fax: (510) 495-2535
Website: Karpen Lab

Lab Members

Principal Scientist
Karpen, Gary

Colmenares, Serafin
Zhang, Weiguo

Postdoctoral Fellows
Janssen, Aniek
Langley, Sasha
Swenson, Joel

Senior Research Associates
Acevedo, David
Kennedy, Cameron

Research/Technical Assistants
Vivar, Maria

Graduate Students
Beier, Nicole
Mills, Wilbur Kyle
Strom, Amy