Peter Hollenhorst Lab
Ph.D., University of Wisconsin, 2002
Assistant Professor of Biochemistry and Molecular Biology
Office Phone: (812) 855-1151
Lab Phone: (812) 856-7608
Cancer can be considered a disease of improper gene expression. In the Hollenhorst lab we are interested in understanding how genomic sequence dictates gene expression and how this process goes awry in cancer. The critical link between the DNA sequence of a genomic regulatory element and the protein machinery that transcribes DNA to RNA is the sequence-specific DNA binding transcription factor. These proteins bind to target sequences in promoters and enhancers, can respond to signaling pathways, and can either promote or inhibit the transcription of nearby genes.
Although we can identify DNA sequence preferences for transcription factors in vitro, this information has not been sufficient to predict transcription factor binding sites in the human genome. One complicating factor that makes such bioinformatic predictions difficult is that most transcription factors do not bind to unique DNA sequences. In fact most human transcription factors belong to “families” that have homologous DNA binding domains and share DNA sequence preferences. One example is the ETS family of 27 human transcription factors that all bind to a similar sequence that includes the core GGA(A/T). Despite the potential for all the members of this family to target the same genomic sequences, genetic studies indicate that each family member has a unique biological function indicating unique target genes.
Understanding how ETS proteins target unique genes is important for understanding their critical role in cancer. Chromosomal rearrangements that alter the expression and/or function of ETS proteins are found in a number of cancers including more than half of prostate tumors, almost all cases of Ewing’s sarcoma, and occasionally in leukemia. However, only a subset of the ETS genes promote cancer. In fact some family members may act as tumor suppressors. Thus a major interest of the lab is to understand the mechanisms that allow specific oncogenic functions within the ETS family.
In the Hollenhorst lab we use a variety of approaches to understand mechanisms of ETS protein specificity:
We use chromatin-immunoprecipitation/next generation sequencing (ChIP-seq) to identify the genomic targets of ETS genes in vivo. Bioinformatics analysis of these results allows us to identify sequences important for both specific and redundant DNA binding within the ETS family.
We use biochemical assays with purified proteins to validate the models of ETS protein/DNA interactions that are predicted by our bioinformatic work. This approach also allows us to dissect the mechanisms of these functions in greater detail.
We express wild-type and mutant ETS genes in cell culture systems to test the function of these proteins on gene expression and to assess oncogenic potential.
Selected publications for further information:
Hollenhorst, P.C., Ferris, M.W., Hull, M.A., Chae, H., Kim, S., and B.J. Graves. (2011). Oncogenic ETS proteins mimic activated RAS/MAPK signaling in prostate cells. Genes & Development 25: 2147-2157
Hollenhorst, P.C., McIntosh, L.P., and B.J. Graves. (2011). Genomic and biochemical insights into the specificity of ETS transcription factors. Annual Review of Biochemistry 80: 437-71.
Hollenhorst, P.C., Paul, L., Ferris, M.W., and B.J. Graves. (2011). The ETS gene ETV4 is required for anchorage-independent growth and a cell proliferation gene expression program in PC3 prostate cells. Genes and Cancer 1: 1044-1052.
Hollenhorst, P.C., Chandler, K.J., Poulsen, R.L., Johnson, W.E., Speck, N.A., and B.J. Graves (2009). DNA specificity determinants associate with distinct transcription factor functions. PLoS Genetics 5(12):e1000778.
Gangwal, K., Sankar, S., Hollenhorst, P.C., Kinsey, M., Haroldsen, S.C., Shah, A.A., Boucher, K.M., Watkins, W.S., Jorde, L.B., Graves, B.J., and S.L. Lessnick (2008). Microsatellites as EWS/FLI response elements in Ewing’s sarcoma. Proc Nat Acad Sci USA 105(29):10149-10154.
Hollenhorst, P.C., Shah, A.A., Hopkins, C., and B.J. Graves (2007). Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes & Development 21(15):1882-1894.
Hollenhorst, P.C., Jones, D.A., and B.J. Graves (2004). Expression profiles frame the promoter specificity dilemma of the ETS family of transcription factors. Nucleic Acids Research 32(18):5693-5702.