Faculty

The Kerppola laboratory uses original experimental approaches to investigate molecular processes in living cells and the architectures of nucleoprotein complexes. Current projects in the laboratory include:

1. Fluorescence resonance energy transfer analysis of nucleoprotein complex architecture and dynamics. We investigate the role of the orientation of heterodimer binding in transcription regulation. We hypothesize that the orientation of heterodimer binding influences cooperative interactions with proteins that bind to adjacent regulatory elements. These studies take advantage of the gel-based fluorescence resonance energy transfer (gelFRET) approach developed in the laboratory.

2. Roles of transcription factor conformation in cooperative gene regulation. The conformations of many transcription factors change upon binding to DNA. We hypothesize that the conformation and function of a transcription factor depends on the sequence of the DNA recognition element. These studies focus on analysis of combinatorial transcription factor interactions that have been identified by the laboratory.

3. Visualization of transcription factor interactions in living cells. A multitude of interactions between transcription regulatory proteins have been identified using in vitro binding assays and genetic screens. We investigate protein interactions in living cells in order to study their regulation in the normal cellular environment. These studies take advantage of the bimolecular fluorescence complementation (BiFC) assay developed in the laboratory.

4. Quantitative analysis of the competition among alternative interaction partners for complex formation in cells. Most proteins can form complexes with many different interaction partners in cells. Many of these interactions are mediated by overlapping contact interfaces, and are therefore mutually exclusive. We use the multicolor BiFC assay to measure the relative efficiencies of complex formation by alternative interaction partners in living cells.

5. Investigation of the roles of ubiquitin-family peptide modifications in transcription factor function. Many proteins are covalently modified by ubiquitin-family peptides. Ubiquitination has been found to have a variety of effects on the functions of the modified proteins. We use the ubiquitin mediated fluorescence complementation (UbFC) assay developed in the laboratory to investigate the effects of ubiquitination on the functions of specific transcription regulatory proteins in cells.

Representative Publications

1. Vincenz, C. and Kerppola, TK, "Different polycomb group CBX family proteins associate with distinct regions of chromatin using non-homologous protein sequences," Proc. Natl. Acad. Sci. U.S.A.,2008, 105, 16572.
[Abstract] [PDF]

2. Ikeda, H and Kerppola, TK, "Lysosomal localization of ubiquitinated Jun requires multiple determinants in a lysine-27 linked polyubiquitin conjugate", Molecular Biology of the Cell, 2008, 19, 4588.
[Abstract] [PDF]

3. Ren, X., Vincenz, C., and Kerppola TK., "Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation", Molecular and Cellular Biology, 2008, 28, 2884.
[Abstract] [PDF]

4. Kerppola, T.K., "Visualization of molecular interactions by flourescence complementation", Nat. Rev. Mol. & Cell Biol., 2006, 7, 449.
[Abstract] [PDF]

5. Fang, D. and Kerppola, T.K., "Ubiquitin-mediated Fluorescence Complementation Reveals that Jun Ubiquitinated by Itch/AIP4 is Localized to Lysosomes", Proc. Natl. Acad. Sci. USA, 2004, 101, 14782.
[Abstract] [PDF]

6. Grinberg, A.V., Hu, C-D. and Kerppola, T.K., "Visualization of Myc/Max/Mad Family Dimers and the Competition for Dimerization in Living Cells", Mol. Cell. Biol., 2004, 24, 4294.
[Abstract] [PDF]

7. Hu, C-D. and Kerppola, T.K., "Simultaneous Visualization of Multiple Protein Interactions in Living Cells Using Multicolor Fluorescence Complementation Analysis", Nature Biotech., 2003, 21, 539.
[Abstract] [PDF]

8. Hu, C-D., Chinenov, Y. and Kerppola, T.K., "Visualization of Interactions among bZIP and Rel Family Proteins in Living Cells using Bimolecular Fluorescence Complementation", Mol. Cell, 2002, 9, 789.
[Abstract] [PDF]