My research program is focused on three inter-related areas:

1) Understanding fundamental aspects of protein-DNA recognition
2) Engineering artificial transcription factors for targeted gene regulation and modification
3) Developing selection technologies to characterize and engineer protein-DNA interactions

Protein-DNA recognition - Our research on protein-DNA recognition is focused primarily on two of the most abundant families of DNA-binding domains in metazoans:

Cys2His2 Zinc fingers & Homeodomains

We have recently performed the first comprehensive analysis of homeodomain specificities in a metazoan (D. melanogaster – fruit fly) in collaboration with Michael Brodsky (UMMS-PGFE) & Gary Stormo (Wash. U) (Noyes et al., Cell 2008). Using this information we can build simple qualitative models of recognition that allow the design of homeodomains with novel DNA-binding specificity. This dataset can also be used to broadly predict the specificity of family members from other species (see ural.wustl.edu/flyhd). We continue to build upon this work to understand fundamental aspects of DNA-recognition for the homeodomain and zinc finger families with the goal of broadly and accurately predicting the specificity of naturally-occurring family members in all species. These studies will also provide a valuable resource for understanding specificity determinants within each family for rationally engineering the specificity of these DNA-binding domains.

B1H selection systems - We continue to develop a bacterial one-hybrid system for rapidly characterizing the DNA-binding specificities of sequence-specific transcription factors, both naturally-occurring and engineered. Using this technology we intend to characterize all of the sequence-specific transcription factors in the D. melanogaster genome in collaboration with the laboratory of Michael Brodsky (UMMS – PGFE). This dataset will be used to unravel transcription factor regulatory networks within the fly in collaboration with Saurabh Sinha (UI-Urbana Champaign). We have already begun building computational tools to allow the scientific community to identify cis-regulatory modules using clusters of phylogenetically conserved binding sites for the ~15% of the TFs in the fly genome that we have characterized to date (GenomeSurveyor - biotools.umassmed.edu/genomesurveyor).

ZFNs in Zebrafish - We have utilized our selection technology to create zinc finger nucleases that recognize specific genes in the Zebrafish genome in collaboration with Nathan Lawson (UMMS – PGFE). Zinc finger nucleases (ZFNs) are tailor-made restriction endonucleases that can generate a double-stranded break at a specific DNA sequence defined by the specificity of the attached zinc fingers. Using this technology we have made the first targeted gene knockouts in the zebrafish (Meng et al. Nat. Biotech 2008). We continue to develop these DNA-targeting and cleavage tools with the goal of creating an accessible resource for model organism communities that will allow them to disrupt, or modify, a desired gene in any model organism. This technology should revolutionize reverse genetic approaches in most model organisms and may allow the straightforward creation of tailor-made human disease models with profound implications for the development of treatments for a variety of diseases.