John K. Kim, Ph.D.

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

6183A LSI
210 Washtenaw Ave.
Ann Arbor
Research Interests: 

The research program in my lab is focused on elucidating mechanisms of post-transcriptional gene silencing. Three related areas comprise these efforts. First, we seek to understand the target silencing mechanisms mediated by microRNAs and other classes of endogenous small RNAs through genetic, biochemical, and genomic approaches. Second, because many of these post-transcriptional mechanisms entail regulation at the mRNA 3’ untranslated region (UTR), we investigate the dynamic expression of 3’UTR isoforms during development, their tissue-specific signatures, and how 3’ UTR isoforms are differentially targeted by microRNAs. Finally, as RNA-binding proteins (RBPs) play critical roles in all small RNA-mediated regulatory mechanisms, we investigate known and novel RBPs that collaborate with small RNAs to execute target silencing and explore the global impact of protein-RNA interactions using high-throughput, large-scale methods.

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
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: 

Billi, A.C.*, Freeberg, M.A.*, Day, A.D., Chun, S.Y., Khivansara, V., and Kim, J.K. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genetics 9(3): e1003392 (2013).

Freeberg, M.A.*, Han, T.*, Moresco, J.J., Kong, A., Yang, Y-C., Lu, Z.J., Yates III, J.R., and Kim, J.K. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology 14(2):R13 (2013). PubMed Link

Tabach, Y., Billi, A.C.*, Hayes, G.D.*, Newman, M.A., Zuk, O., Gabel, H., Kamath, R., Yacoby, K., Chapman, B., Garcia, S.M., Borowsky, M., Kim, J.K., and Ruvkun, G. Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Nature 493: 694-698 (2013). PubMed Link

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 336: 1448-1451 (2012). PubMed Link

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(4): e1002617 (2012). PubMed Link

Billi, A.C., Freeberg, M.A., Kim, J.K. piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Genome Biology 13(7): 164 (2012). PubMed Link

modENCODE Consortium (Gerstein, M.B. et al.,). Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project. Science 330: 1775-1787 (2010). PubMed Link

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: 432-435 (2010). PubMed Link

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: 1234-1235 (2010). PubMed Link

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: 18674-18679 (2009). PubMed Link

Friedländer, M.R., Adamidi, C., Han, T., Lebedeva, S., Isenbarger, T.A., Hirst, M., Marra, M., Nusbaum, C., Lee, W.L., Sánchez Alvarado, A., Kim, J.K., and Rajewsky, N. High-resolution discovery and profiling of planarian small RNAs. Proc. Natl. Acad. Sci. USA 106: 11546-11551 (2009). PubMed Link

modENCODE Consortium (Celniker, S.E. et al.,). Unlocking the secrets of the genome. Nature 459: 927-930 (2009). PubMed Link

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

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

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., and Ruvkun, G. Functional genomic analysis of RNA interference in C.elegans. Science 308: 1164-1167 (2005). PubMed Link

Kim, J., Krichevsky, A., Grad, Y., Hayes, G.D., Kosik, K.S., Church, G.M., and Ruvkun, G. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl. Acad. Sci. USA 101: 360-365 (2004). PubMed Link

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

*equal contribution


Kim, J., Huang, W.P., Stromhaug, P.E., Klionsky, D.J. 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 (2002).

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

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

Kim, J., Kamada, Y., Stromhaug, P., Guan, J., Hefner-Gravink, A., Baba, M., Dunn, W., Ohsumi, Y., Klionsky, D.J. Cvt9p/Gsa9p functions in sequestering selective cytosolic cargo destined for the vacuole. Journal of Cell Biology 153: 381-396 (2001).

Kim, J., Huang, W.P., Klionsky, D.J. Membrane recruitment of Aut7p in the autophagy and Cvt pathways requires Aut1p, Aut2p and the Apg conjugation system. Journal of Cell Biology 152: 51-64 (2001).

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

Abeliovich, H., Dunn, W., Kim, J., Klionsky, D.J. Dissection of autophagosome biogenesis into distinct nucleation and expansion steps. Journal of Cell Biology 151: 1025-1034 (2000).

Huang, W.-P., Scott, S.V., Kim, J., Klionsky, D.J. 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 (2000).

Noda, T.*, Kim, J.*, Huang, W.P., Baba, M., Tokunaga, C., Ohsumi, Y., Klionsky, D.J. Apg9/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. Journal of Cell Biology 148: 465-480 (2000). *equal contribution

Kim, J. and Klionsky, D.J. Autophagy, Cvt pathway, and pexophagy in yeast and mammalian cells. Annual Review of Biochemistry 69: 303-342 (2000).

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

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

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

Kim, J., Alizadeh, P., Harding, T., Hefner-Gravink, A., Klionsky, D.J. 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 (1996).

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. Identification and characterization of glima 38, a glycosylated islet cell membrane antigen, which together with GAD65 and IA2 mark the early phases of autoimmune response in type 1 diabetes. Journal of Clinical Investigation 7: 2772-2283 (1996).

Kim, J., Namchuk, M., Bugawan, D., Fu, Q., Jaffe, M., Shi, Y., Aanstoot, H., Turck, C.W., Erlich, H., Lennon, V., Baekkeskov, S. Higher autoantibody levels and recognition of a linear N-terminal epitope in the autoantigen GAD65 distinguish stiff-man syndrome from insulin dependent diabetes mellitus. Journal of Experimental Medicine 180: 595-606 (1994).

Kim, J., Richter, W., Aanstoot, H.J., Shi, Y., Fu, Q., Rajotte, R., Warnock, G., Baekkeskov, S. Differential expression of GAD65 and GAD67 in human, rat, and mouse pancreatic islets. Diabetes 42: 1799-1808 (1993).

Aanstoot, H.J., Michaels, A., Christgau, S., Shi, Y., Kim, J., Baekkeskov, S. Stiff-Man Syndrome and Type 1 Diabetes Mellitus: Similarities and Differences in Autoimmune Reactions. Motor Unit Hyperactivity States, ed. Layzer, R.B.: 53-67, Raven Press (1993).

Baekkeskov, S., Aanstoot, H.J., Fu, Q., Jaffe, M., Kim, J., Quan, J., Richter, W., Shi, Y. The glutamic acid decarboxylase and 38kD autoantigens in type 1 diabetes: Aspects of structure and epitope recognition. Autoimmunity 15: 24 (1993).