Joung Lab (Summer 2007), l to r:
K. Joung, C. Ramirez, S. Beganny, M. Maeder, J. Foley, L. Le
  • Research Interests:
    Our laboratory has developed robust protein engineering methods for constructing artificial "designer" DNA-binding domains. Our efforts focus on Cys2His2 zinc fingers, the most common structural motif found in eukaryotic transcription factors. We are also developing engineered zinc finger proteins for applications in biological research and gene therapy.

    Engineering "designer" zinc fingers with novel DNA-binding specificities
    The Joung lab is a founding member of The Zinc Finger Consortium (http://www.zincfingers.org). As part of this collaborative effort, we are developing robust selection and design methods for rapidly engineering synthetic zinc finger domains with novel, defined DNA-binding specificities. Designer zinc fingers can be used to target functional domains to specific genomic loci in cells (see below) and analysis of the amino acid sequences and specificities of these artificial fingers will be useful for developing algorithms to predict the DNA-binding specificities of naturally occurring zinc finger domains.

    Engineered zinc finger nucleases for targeted, highly efficient genome manipulation
    Zinc finger nucleases (ZFNs), consisting of designer zinc fingers fused to a non-specific endonuclease domain, can be used to introduce targeted DNA alterations with high efficiency at specific genomic loci in mammalian, plant, zebrafish, or Drosophila cells. These alterations result from repair of ZFN-induced double-stranded DNA breaks by normal cellular repair processes (non-homologous end-joining or homologous recombination). On-going projects in the lab are aimed at developing the ZFN genome modification methodology and using it for applications in biological research and gene therapy.

    Altering cellular phenotypes using combinatorial zinc finger transcription factor libraries
    We have recently constructed large combinatorial libraries of zinc finger domains which can be fused to various transcriptional regulatory domains (e.g.--activation or repression domains). We are introducing these libraries into human cells to induce specific desired phenotypes and cellular states.
  • Joung Lab: (Lab Phones: 617-726-5689 and 617-643-3647)

    • J. Keith Joung, M.D., Ph.D.
      Assistant Professor of Pathology, Harvard Medical School
      Director, Molecular Pathology Unit, and Assistant Pathologist, Massachusetts General Hospital
      Tel: 617-726-9462 | Fax: 617-726-5684
    • Stacey Thibodeau Beganny
      Senior Research Technologist and Laboratory Manager
      sbeganny@partners.org
  • Publications:
    • Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB, Cathomen T, Voytas, DF, Joung JK. Rapid "Open-Source" Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification. Mol. Cell. 2008; 31: 294-301.
    • Cathomen T, Joung JK. Zinc-finger nucleases: the next generation emerges. Mol Ther. 2008; 16: 1200-1207.
    • Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK. Unexpected failure rates for modular assembly of engineered zinc-fingers. Nat Methods. 2008;5(5): 374-375.
    • Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH. Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol Ther. 2008 Apr;16(4):707-17. Epub 2008 Mar 4.
    • Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK,Cathomen T. DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol Ther. 2008 Feb;16(2):352-8. Epub 2007 Nov 20.
    • Thibodeau-Beganny S, Joung JK. Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system. Methods Mol Biol. 2007;408:317-34.
    • Meng X, Thibodeau-Beganny S, Jiang T, Joung JK, Wolfe SA. Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method. Nucleic Acids Res. 2007;35(11):e81. Epub 2007 May 30.
    • Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D. Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W599-605. Epub 2007 May 25.
    • Wright DA, Thibodeau-Beganny S, Sander JD, Winfrey RJ, Hirsh AS, Eichtinger M, Fu F, Porteus MH, Dobbs D, Voytas DF, Joung JK. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc. 2006;1(3):1637-52.
    • Giesecke AV, Fang R, Joung JK. Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers. Mol Syst Biol. 2006;2:2006.2011. Epub 2006 Mar 21.
    • Meng X, Smith RM, Giesecke AV, Joung JK, Wolfe SA. Counter-selectable marker for bacterial-based interaction trap systems. Biotechniques. 2006 Feb;40(2):179-84.
    • Vallet-Gely I, Donovan KE, Fang R, Joung JK, Dove SL. Repression of phase-variable cup gene expression by H-NS-like proteins inPseudomonas aeruginosa. Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11082-7. Epub 2005 Jul 25.
    • Serebriiskii IG, Fang R, Latypova E, Hopkins R, Vinson C, Joung JK, Golemis EA. A combined yeast/bacteria two-hybrid system: development and evaluation. Mol Cell Proteomics. 2005 Jun;4(6):819-26. Epub 2005 Mar 20.
    • Nguyen-Hackley DH, Ramm E, Taylor CM, Joung JK, Dervan PB, Pabo CO. Allosteric inhibition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands. Biochemistry. 2004 Apr 6;43(13):3880-90.
    • Thibodeau SA, Fang R, Joung JK. High-throughput beta-galactosidase assay for bacterial cell-based reporter systems. Biotechniques. 2004 Mar;36(3):410-5.
    • Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK. Highly specific zinc finger proteins obtained by directed domain shuffling andcell-based selection. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12271-6. Epub 2003 Oct 3.
    • Joung JK. Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system. J Cell Biochem Suppl. 2001;Suppl 37:53-7. Review.
    • Joung JK, Ramm EI, Pabo CO. A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7382-7.
    • Dove SL, Joung JK, Hochschild A. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature. 1997 Apr 10;386(6625):627-30.
  • Former Lab Members:

    • Sandra Fay-Richard, Lab Manager
    • Jessica Hurt, Research Technologist
    • Andrew Hirsh, Post-Doctoral Fellow
    • Rui Fang, Post-Doctoral Fellow
    • Astrid Giesecke, Graduate Student
    • Edouard Kengni, Volunteer Scientist
    • Carl Gobel, Undergraduate Summer Student
    • Nicolas Bonnaig, Undergraduate Summer Student
    • Sandra Ahn, Undergraduate Summer Student
    • Tao Jiang, Ph.D., Post-Doctoral Fellow
    • Magdalena Eichtinger, M.D., Post-Doctoral Fellow
    • Megan McSweeney, Research Technician