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
Our lab uses genomics and bioinformatics approaches to develop hypotheses that we then test with biochemical and cell biological assays. We focus on two major research questions:
1. Understanding specificity in transcription factor families.
The regions of the human genome that encode the instructions for gene regulation (where and when a gene should be expressed) are vastly larger and more complex than protein coding regions, and we currently have little understanding of their function. These cis-regulatory elements are interpreted by sequence specific interactions with proteins such as transcription factors. 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 28 human transcription factors that, in vitro, all bind to the sequence (C/A)GGA(A/T)G. Despite the potential for all the members of this family to bind the same places in the genome, genetic studies indicate that each family member has a unique biological function - thereby indicating unique target genes. Thus the question: How do members of a transcription factor family attain unique functions despite overlapping DNA sequence preference?
To address this question we map the places in the genome of live cells where members of ETS and other transcription factor families bind. (We use chromatin-immunoprecipitation/next generation sequencing, or ChIP-seq). Bioinformatics analysis of these results allows us to ask if family members bind the same places, or have unique targets. If there are unique targets, we can identify sequence motifs that dictate the functions of individual family members. We then 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.
2. Deciphering the role of ETS family transcription factors in cancer.
ETS family transcription factor play a major role in human disease, particularly cancer. Chromosomal rearrangements or amplifications that alter the expression and/or function of ETS proteins are among the most common mutations in human cancer and occur in more than half of prostate tumors, 40% of melanomas, almost all cases of Ewing’s sarcoma, and in some leukemias. 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.
We have recently shown that a major function of ETS proteins in cancer is to drive cellular migration and invasion through cis-regulatory elements that have binding sites for both ETS and AP-1 family transcription factors. We have shown that these ETS/AP-1 sequence elements can mediate gene expression responses to signaling from the RAS/ERK, PI3K/AKT, and potentially other signaling pathways, depending on which ETS and AP-1 family member is bound. Understanding how this cis-regulatory element works is a current focus in the lab.
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.