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Tom Kerppola

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Primary Appointment: Biological Chemistry Dept
Other PIBS Depts.: Biophysics
PubMed Name: Kerppola T.K.
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  Our laboratory is interested in the regulation of transcription in mammalian cells. The differential regulation of each gene is essential for the appropriate growth and development of the organism. This task is accomplished through the coordinated function of multiple transcription regulatory proteins at each promoter. The selective regulation of gene expression requires that transcription factors are able to interact with each other in many different combinations, yet that their interactions are specific such that they can only occur at particular regulatory elements or in response to specific stimuli. Thus, the key to understanding transcription regulatory specificity is discovery of the mechanisms that control transcription factor interactions.

We focus on investigation of networks of protein interactions and studies of the architectures of nucleoprotein complexes. We have developed many new methods for the study of these areas that enable visualization of protein interactions in living cells and analysis of the structural organization and dynamics of transcription factor complexes in vitro. These approaches provide unique opportunities for us to investigate molecular processes in a physiological context. The goal of our studies is to understand how different combinations of proteins cooperate to produce distinct functional outcomes in different cell types and in response to different extracellular stimuli. In these studies, we focus on the functions of proto-oncogene transcription factors related to c-fos, c-jun, c-maf, c-myc and NFAT in the regulation of developmental and immunomodulatory genes.

Our previous studies of transcription factor interactions have produced several discoveries that have fundamentally altered our understanding of transcription regulatory mechanisms. David Leonard developed the gel based fluorescence resonance energy transfer (gelFRET) assay, and found that Fos-Jun heterodimers bound to AP-1 sites in a preferred orientation. Vladimir Ramirez-Carrozzi found that electrostatic interactions with sequences flanking the AP-1 site controlled the orientation of Fos-Jun binding and determined the cooperativity of DNA binding and transcription activation with the nuclear factor of activated T cells (NFAT1). Chang-Deng Hu developed the bimolecular fluorescence complementation (BiFC) assay and demonstrated that Fos-Jun heterodimers form more efficiently than Fos-ATF2 or Jun-ATF2 heterodimers when all three proteins are expressed in the same cell. Asya Grinberg found that Myc and Mad family proteins compete with different efficiencies for dimerization with Max in cells, and that they can all interact with Smad family transcription factors. Deyu Fang developed the ubiquitin-mediated fluorescence complementation (UbFC) assay and discovered that ubiquitinated Jun is translocated into lysosomes for degradation. Nirmala Rajaram discovered that Maf and Sox family proteins cooperate to regulate crystallin gene expression, and that a mutation in Maf that causes cataract alters the subnuclear localization and transcriptional activity of the complex. Claudius Vincenz developed methods for isolation of BiFC stabilized complexes (iBiSC) and demonstrated that different polycomb group proteins bind to different chromosomal regions. Xiaojun Ren identified new polycomb group protein interaction partners and demonstrated that they regulate the specificity of polycomb group binding to chromatin and their transcriptional activities. Present laboratory members are continuing to make new discoveries that add to our understanding of transcription regulatory mechanisms.