University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Min Kyu Kim, PhD

Min Kyu Kim, PhD

Assistant Professor, Cellular & Molecular Pharmacology/QBI, UCSF

Cancer Center Program Memberships

Breast Oncology | Cancer Genetics

Research Summary

Protein Interaction Networks Governing Cell Differentiation

Stem cells are pluripotent to differentiate into various cell types in the body. Thus, analyzing each differentiation process using stem cells is fundamental not only to understand its basic mechanisms but also to take advantage of stem cells for therapeutic purposes. My research will investigate protein differential regulation and protein-protein interactions, using the large-scale proteomics and genomics, to dissect functions of protein complexes during cellular differentiation as they are formed and expressed. This study may allow us to identify a novel key regulator(s) of significant medical relevance for multiple cellular differentiation pathways (especially for cancer research and treatment).

Transcription Termination and RNA Processing

Proteins of different activities are often derived from a single gene by alternative polyadenylation and termination, and many bacterial operons are controlled by attenuation, which manifest the importance of transcription termination in gene regulation. However, the mechanisms that terminate transcription are less well understood. The goal of this research is to define the functional interactions between various protein factors and RNA polymerases to understand the regulation of transcription termination and its fundamental roles in gene expression and RNA 3’-end processing. Ultimately, this study may be able to lead us to manipulate termination, so that we can develop potential therapies for genetic disorders caused by aberrant termination.

Education

Korea Advanced Institute of Science and Technology (KAIST), Korea, B.Sc., 02/1992, Biology (Cum laude)
Seoul National University, Korea, M.S,. 02/1995, Molecular Biology
Seoul National University, Korea, Ph.D., 08/2000, Molecular Biology
Seoul National University, Korea, Postdoc, 02/2001, Molecular Biology
Harvard Medical School, MA, USA, Postdoc, 12/2009, Biochemistry/Proteomics


Professional Experience

  • 09/2000 – 02/2001
    Postdoctoral Fellow, Seoul National University
  • 03/2001 – 12/2009
    Postdoctoral Fellow, Harvard Medical School 
  • 01/2010 – 12/2014
    WCU Assistant Professor, Biophysics & Chemical Biology, Seoul National University
  • 09/2013 – 12/2014
    Faculty Investigator, Center for RNA Research, Institute for Basic Science, Korea
  • 01/2015 – present
    Adjunct Assistant Professor, Cellular & Molecular Pharmacology/QBI, UCSF

Honors & Awards

  • 1992
    Cum laude, Korea Advanced Institute of Science and Technology, Korea
  • 1995 – 1996
    Pre-doctoral Fellowship for Future Researchers, Korea Research Foundation
  • 2004
    BCMP Discovery of the Year Award, Harvard Medical School
  • 2005 – 2007
    Charles A. King Trust Post-Doctoral Fellowship, the Medical Foundation, MA
  • 2016 – 2017
    Breast Cancer Research Fund (BCRF) Award, Helen Diller Family Comprehensive Cancer Center, UCSF
  • 2016 – 2017
    Program for Breakthrough Biomedical Research (PBBR) Award, UCSF

Selected Publications

  1. Kim K, Heo DH, Kim I, Suh JY, Kim M. Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome. J Biol Chem. 2016 Jun 17; 291(25):13229-42.
    View on PubMed
  2. Park J, Kang M, Kim M. Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1. Nucleic Acids Res. 2015 Mar 11; 43(5):2625-37.
    View on PubMed
  3. Heo DH, Yoo I, Kong J, Lidschreiber M, Mayer A, Choi BY, Hahn Y, Cramer P, Buratowski S, Kim M. The RNA polymerase II C-terminal domain-interacting domain of yeast Nrd1 contributes to the choice of termination pathway and couples to RNA processing by the nuclear exosome. J Biol Chem. 2013 Dec 20; 288(51):36676-90.
    View on PubMed
  4. Lunde BM, Reichow SL, Kim M, Suh H, Leeper TC, Yang F, Mutschler H, Buratowski S, Meinhart A, Varani G. Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat Struct Mol Biol. 2010 Oct; 17(10):1195-201.
    View on PubMed
  5. Kim M, Suh H, Cho EJ, Buratowski S. Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J Biol Chem. 2009 Sep 25; 284(39):26421-6.
    View on PubMed
  6. Vasiljeva L, Kim M, Mutschler H, Buratowski S, Meinhart A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol. 2008 Aug; 15(8):795-804.
    View on PubMed
  7. Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell. 2008 Feb 15; 29(3):313-23.
    View on PubMed
  8. Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. Dynamics of replication-independent histone turnover in budding yeast. Science. 2007 Mar 9; 315(5817):1405-8.
    View on PubMed
  9. Kim M, Vasiljeva L, Rando OJ, Zhelkovsky A, Moore C, Buratowski S. Distinct pathways for snoRNA and mRNA termination. Mol Cell. 2006 Dec 8; 24(5):723-34.
    View on PubMed
  10. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 2005 Oct; 3(10):e328.
    View on PubMed
  11. Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature. 2004 Nov 25; 432(7016):517-22.
    View on PubMed
  12. Kim M, Ahn SH, Krogan NJ, Greenblatt JF, Buratowski S. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J. 2004 Jan 28; 23(2):354-64.
    View on PubMed
  13. Ahn SH, Kim M, Buratowski S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3' end processing. Mol Cell. 2004 Jan 16; 13(1):67-76.
    View on PubMed
  14. Nedea E, He X, Kim M, Pootoolal J, Zhong G, Canadien V, Hughes T, Buratowski S, Moore CL, Greenblatt J. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends. J Biol Chem. 2003 Aug 29; 278(35):33000-10.
    View on PubMed
  15. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun; 23(12):4207-18.
    View on PubMed
  16. Kim MJ, Kim M, Park SD. Post-transcriptional regulation of ura4+ gene expression by glucose in Schizosaccharomyces pombe. Mol Cells. 2002 Dec 31; 14(3):437-43.
    View on PubMed
  17. Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol. 2002 Oct; 22(20):6979-92.
    View on PubMed
  18. Jang YK, Kim M, Dai Park S. Fibrillarin binds to a 3' cis-regulatory element in pre-mRNA of uvi15+ in fission yeast. Biochem Biophys Res Commun. 2002 Jun 28; 294(5):1184-90.
    View on PubMed
  19. Cho EJ, Kobor MS, Kim M, Greenblatt J, Buratowski S. Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 2001 Dec 15; 15(24):3319-29.
    View on PubMed
  20. Kim M, Lee W, Park J, Kim JB, Jang YK, Seong RH, Choe SY, Park SD. The stress-activated MAP kinase Sty1/Spc1 and a 3'-regulatory element mediate UV-induced expression of the uvi15(+) gene at the post-transcriptional level. Nucleic Acids Res. 2000 Sep 1; 28(17):3392-402.
    View on PubMed

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