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Our Research

Transcription is a biological process that plays a central role in normal development and homeostasis in multicellular organisms. Transcription factors that bind promoter elements of genes with high affinity and sequence specificity are essential regulators. My laboratory has a longstanding interest in the ETS family of regulatory transcription factors that share DNA binding properties (Hollenhorst et al. 2011) and function as repressors or activators of gene expression. This metazoan gene family includes 28 human paralogs. My research program has taken a multidisciplinary approach to understanding the biology and biochemistry of ETS proteins in normal development and human cancer.

Pathways to Specificity of ETS proteins

ETS Family of Transcription Factors

We have set as a long-term goal to understand how a family of highly related DNA binding factors is utilized in biological regulation using the ETS family as a model system. Do individual ETS proteins have unique roles or are there redundancies of function within the family? Specificity would require both a divergence of functionality of individual family members as well as pathways to direct different family members to different gene promoter targets. We have recently described that there is extensive co-expression of ETS family members in a diverse sampling of human cell types. Genome-wide analysis of promoter targets in several of the cell types shows that, in some cases, there is specific matching between specific ETS proteins and specific targets. In other cases, there is co-occupancy by multiple ETS proteins at a specific promoter (Hollenhorst et al. 2004, 2007, 2009). We are currently investigating mechanisms of specificity for multiple family members including Ets-1, ETV6, ETV1, ETV4 and ETV5.

Regulation of DNA Binding by Autoinhibition Mechanism

dna

Autoinhibition is a phenomenon that involves intramolecular interactions and provides a framework for regulation of protein function (Pufall and Graves 2002). We study the autoinhibitory mechanisms that regulate the DNA binding of members of the ETS family as a route to specificity.  Ets-1 is best understood. Its inhibition is counteracted by a partnership with a second transcription factor, RUNX1 (Goetz et al., 2000). And, a calcium-dependent signaling pathway reinforces the autoinhibition (Cowley and Graves 2000, Pufall et al. 2005). Structural and dynamic studies have led to a detailed mechanism for autoinhibition that illustrates the dynamic nature of proteins and how this property is used in regulation (Garvie et al. 2002; Lee et al. 2005; Pufall et al. 2005). Of particular significance is the finding that unstructured regions can do work and that the mechanism works allosterically. Our investigations of Ets-1 autoinhibition include ongoing collaborations with structural biologist Lawrence McIntosh, University of British Columbia.

The ETS protein ETV6 displays a mechanism of autoinhibition distinct from Ets-1.  An inhibitory helix sterically blocks the binding surface and must unfold upon DNA binding (Green et al. 2010, Coyne et al. 2012,  De et al., 2014). The inhibition is compensated for by cooperative binding between multiple ETV6 species, which can bind in tandem on DNA due to the self-association properties of the PNTdomain.

We are currently investigating autoinhibition of the ETV1, 4, and 5 subfamily of ETS proteins. 

ETS Factors and Human Cancers

We use these biochemical and genomics approaches to investigate the role of the ETS family in human cancers. Nuclear oncogenes are most often transcription factors that cause inappropriate gene expression. The ETS family illustrates this oncogenic potential. The genes that encode several ETS proteins, ERG, FLI and ETV6, are altered by chromosome translocations that associate with specific human cancers. Classes of sarcoma, leukemia, and prostate cancer are driven by these altered ETS genes. ETS proteins are also targets of Ras-dependent signaling, a growth control pathway frequently mutated to be superactivated in human cancers. Using genomics approaches we are identifying the target genes of these oncogenic ETS factors. We are also investigating critical roles of ETS factors in chromatin remodeling by identifying co-factors that associate with these oncogenic ETS factors.