John K. Kim, Ph.D.

Assistant Professor of Human Genetics
Assistant Research Professor, Life Sciences Institute

6183A LSI

210 Washtenaw Ave.

Ann Arbor

48109-2216

Phone:

734-615-9915

Fax:

734-615-5493

Email:

jnkim@umich.edu

Lab Website:

http://www.lsi.umich.edu/facultyresearch/labs/kim

Research Interests:

Our lab studies how microRNAs and other endogenous classes of small RNAs regulate fundamental biological processes including neuronal and muscle development, germline maintenance, and oncogenic cell proliferation. Using functional genomic, genetic, biochemical, and cell biology strategies, our lab investigates the molecular mechanisms of small RNA biogenesis and function. We also investigate the role of RNA binding proteins (RBPs) both at the whole-transcriptome level and particular RBPs that function in the microRNA pathway.

Honors and Awards:

2009 - 2013 Pew Scholar in the Biomedical Sciences

2006 Biological Sciences Scholar, University of Michigan

2006 MGH Fund for Medical Discovery Fellowship

2003 - 2006 Helen Hay Whitney Postdoctoral Fellowship

Education:

2001 - 2006 Postdoctoral Fellowship, Harvard Medical School, MGH

1994 - 2000 Ph.D., Biochemistry and Molecular Biology, U.C., Davis

1990 - 1994 Research associate, U.C., San Francisco

1986 - 1990 B.S., Molecular Biophysics and Biochem., Yale University

Selected Publications:

Moissiard, G., Cokus, S., Cary, J., Feng, S., Billi, A.C., Stroud, H., Husmann, D., Zhan, Y., Lajoie, B.R., McCrod, R.P., Hale, C.J., Feng, W., Michaels, S.D., Frand, A.R., Pellegrini, M., Dekker, J., Kim, J.K., and Jacobsen, S. MORC family ATPases required for heterochromatin condensation and gene silencing. Science (in press).

Billi, A.C., Alessi, A.F., Khivansara, V., Han, T., Freeberg, M., Mitani, S., and Kim, J.K. The Caenorhabditis elegans HEN1 ortholog, HENN-1, methylates and stabilizes select subclasses of germline small RNAs. PLoS Genetics 8: e1002617 (2012).

modENCODE Consortium (Gerstein, M.B. et al.,). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project. Science 330: 1775-87 (2010).

Mangone, M., Manoharan, A.P., Thierry-Mieg, D., Thierry-Mieg, J., Han, T., Mackowiak, S., Mis, E., Zegar, C., Gutwein, M.R., Khivansara, V., Salehi-Ashtiani, K., Harkins, T. Bouffard, P., Suzuki, Y., Sugano, S., Kohara, Y., Rajewsky, N., Piano, F., Gunsalus, K.C., and Kim, J.K. The landscape of C. elegans 3' UTRs. Science 329: 432-5 (2010).

Han, T., Manoharan, A.P., Harkins, T.T., Bouffard, P., Fitzpatrick, C., Chu, D.S., Thierry-Mieg, D., Thierry-Mieg, J., and Kim, J.K. 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in C. elegans. Proc. Natl. Acad. Sci. USA 106(44):18674-9 (2009).

modENCODE Consortium. Unlocking the secrets of the genome. Nature 459:927-30 (2009).

Friedlander, M.R., Adamidi, C., Han, T., Lebedeva, S., Isenbarger, T.I., Hirst, M., Marra, M., Nusbaum, C., Lee, W.L., Jenkins, J., Sanchez Alvarado, A., Kim, J.K., and Rajewsky, N. "High-resolution discovery and profiling of planarian small RNAs." Proc. Natl. Acad. Sci. USA 106(28):11546-51 (2009).

Simon, D.J., Madison, J.M., Connery, A.L., Thompson-Peer, K.L., Soskis, M., Ruvkun, G.B., Kaplan, J.M., Kim, J.K. The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell 133:903-915 (2008).

Wang, D., Kennedy, S., Conte, D., Kim, J.K., Gabel, H.W., Kamath, R.S., Mello, C.C., & Ruvkun, G. (2005). Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature, 436, 593-597.

Kim, J.K., Gabel, H.W., Kamath, R.S., Tewari, M., Pasquinelli, A., Rual, J.F., Kennedy, S., Dybbs, M., Bertin, N., Kaplan, J.M., Vidal,M., & Ruvkun, G. (2005). Functional genomic analysis of RNA interference in C.elegans. Science, 308, 1164-1167.

Kim, J., Krichevsky, A., Grad, Y., Hayes, G.D., Kosik, K.S., Church, G.M., & Ruvkun, G. (2004). Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proceedings of the National Academy of Sciences of the USA, 101, 360-365.

Grad, Y., Aach, J., Hayes, G.D., Reinhart, B.J., Church, G.M., Ruvkun, G., & Kim, J. (2003). Computational and experimental identification of C. elegans microRNAs. Molecular Cell, 11, 1253-1263.

Kim, J., Huang, W.P., Stromhaug, P.E., & Klionsky, D.J. (2002). Convergence of multiple autophagy and cytoplasm-to-vacuole targeting components to a perivacuolar membrane compartment prior to de novo vesicle formation. Journal of Biological Chemistry, 277, 763-773.

Teter, S. A., Eggerton, K.P., Scott, S.V., Kim, J., Fischer, A.M., & Klionsky, D.J. (2001). Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase.Journal of Biological Chemistry, 276, 2083-2087.

Wang, C. W., Kim, J., Huang, W.P., Abeliovich, H., Stromhaug, P.E., Dunn, W.A., & Klionsky, D.J. (2001). Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways. Journal of Biological Chemistry, 276,30442-30451.

Kim, J., Huang, W.P., & Klionsky, D.J. (2001). Membrane recruitment of Aut7p in the autophagy and cytoplasm-to-vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex. Journal of Cell Biology, 152, 51-64.

Kim, J., Kamada, Y., Stromhaug, P.E., Guan, J., Hefner-Gravink, A., Baba, M., Scott, S. V., Ohsumi, Y., Dunn, W. A., & Klionsky, D. J.(2001). Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole. Journal of Cell Biology, 153, 381-396.

Scott, S.V., Guan, J., Hutchins, M.U., Kim, J., & Klionsky, D.J.(2001). Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway. Molecular Cell, 7, 1131-1141.

Huang, W.P., Scott, S.V., Kim, J., & Klionsky, D.J. (2000). The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. Journal of Biological Chemistry, 275, 5845-5851.

Noda, T., Kim, J., Huang, W.P., Baba, M., Tokunaga, C., Ohsumi, Y., & Klionsky, D.J. (2000). Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. Journal of Cell Biology, 148, 465-479.

Abeliovich, H., Dunn, W.A., Kim, J., & Klionsky, D.J. (2000). Dissection of autophagosome biogenesis into distinct nucleation and expansion steps. Journal of Cell Biology, 151, 1025-1033.

Kim, J., Dalton, V.M., Eggerton, K.P., Scott, S.V., & Klionsky, D.J. (1999). Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Molecular Biology of the Cell, 10, 1337-1351.

Kim, J., Scott, S.V., Oda, M.N., & Klionsky, D.J. (1997). Transport of a large oligomeric protein by the cytoplasm to vacuole protein targeting pathway. Journal of Cell Biology, 137, 609-618.

Kim, J., Alizadeh, P., Harding, T., Hefner-Gravink, A., & Klionsky, D.J. (1996). Disruption of the yeast ATH1 gene confers better survival after dehydration, freezing, and ethanol shock: Potential commercial applications. Applied and Environmental Microbiology, 62, 1563-1569.

Aanstoot, H.J., Kang, S.M., Kim, J., Lindsay, L.A., Roll, U., Knip, M., Atkinson, M., Mose-Larsen, P., Fey, S., Ludvigsson, J., Landin, M., Bruining, J., Maclaren, N., Akerblom, H.K., & Baekkeskov, S.(1996). Identification and characterization of glima 38, a glycosylated islet cell membrane antigen, which together with GAD(65) and IA2 marks the early phases of autoimmune response in type 1 diabetes. Journal of Clinical Investigation, 97, 2772-2783.

Kim, J., Namchuk, M., Bugawan, T., Fu, Q., Jaffe, M., Shi, Y.G., Aanstoot, H.J., Turck, C.W., Erlich, H., Lennon, V., & Baekkeskov, S.(1994). Higher autoantibody levels and recognition of a linear NH2-terminal epitope in the autoantigen GAD(65) distinguish stiff man syndrome from insulin-dependent diabetes mellitus. Journal of Experimental Medicine, 180, 595-606.

Kim, J., Richter, W., Aanstoot, H.J., Shi, Y.G., Fu, Q., Rajotte, R., Warnock, G., & Baekkeskov, S. (1993). Differential expression of GAD(65) and GAD(67) in human, rat, and mouse pancreatic islets. Diabetes, 42, 1799-1808.

Review Articles

Irminger-Finger, I., Thomson, J.M., Kim, J.K. (editors). MicroRNAs, a superimposed regulatory network for development and disease. Int J Biochem Cell Biol 42: 1234-5 (2010).

Kim, J., & Klionsky, D.J. (2000). Autophagy, cytoplasm-to-vacuole targeting pathway, and pexophagy in yeast and mammalian cells. Annual Review of Biochemistry, 69, 303-342.

Kim, J., Scott, S.V., & Klionsky, D.J. (2000). Alternative protein sorting pathways. International Review of Cytology, 198,153-201.

Patents

Kim, J., Gabel, H., Kamath, R., Ruvkun, G. (2005). Compositions and Methods that Modulate RNA Interference. Patent application filed. Serial No. 11/106,238.

Baekkeskov, S., Richter, W., Shi, Y., Namchuk, M., Kim, J. (1997). Reagents and Methods for the Diagnosis and Treatment of Diabetes and Stiff Man Syndrome. United States Patent 5,691,448