Almost every disease has a genetic component. Often this information is used only to determine how condemned a person is to develop disease. We would like to use the genetic information to fix the disease. A guiding principle for our work has been to study how nature does what it does, then attempt to use that knowledge to make useful tools to improve public health, either through increased knowledge or therapeutic intervention. Specific research foci in the Segal Lab revolve around engineering custom zinc finger DNA-binding proteins for specific applications. We also continue to make methodological improvements, many of which have been widely adapted in the field.

• Designing permanent inactivators of HIV. We are designing zinc finger nucleases to chop up the integrated DNA form of the HIV provirus without affecting any human sequences. Unlike most other anti-HIV therapies, this approach would permanently inactivate the virus. It should also be useful in patients with viruses that use CXCR4, for whom CCR5 entry inhibitors would be ineffective (ie: most infected patients). We are also developing novel delivery methods.

• Manipulating epigenetic mechanisms in Angelman and Rett Syndromes . These are rare neurogenetic diseases that cause autism-spectrum symptoms, but their genetics has made them the textbook examples of imprinting disorders. We are using zinc finger-based artificial transcription factors to activate the epigenetically silenced genes in these diseases.

• Manipulating genetic variation in Coronary Artery Disease (CAD). Several genetic variations (SNPs) have been recently associated with an increased risk of CAD. We are engineering zinc finger nucleases to engineer defined haplotypes in order to understand the functional role of these variants. Our approach overcomes the historic barrier of trying to study the affects of specific human mutations in a background of millions of other genetic differences between two individuals.

• Detecting bloodborn pathogens. We are developing a microfluidic point-of-care device to detect pathogens based on their genetic sequence. Instead of PCR, we are using our patented sequence-enabled reassembly (SEER) technology for isothermal colorimetric detection.

• High-throughput investigations of zinc finger-DNA interactions. We recently developed a high-throughput assay called Bind-n-Seq, and are using it to study the binding affinity and specificity of engineered and natural zinc finger proteins (of which there are over 700 in human). We are using bioinformatics, protein structure analysis, and biochemistry to understand the zinc finger-DNA recognition code, so that we can predict the binding sites and functions of uncharacterized zinc finger proteins.

Selected Publications

Carroll, D., Morton, J.J., Beumer, K.J. & Segal, D.J. (2006) Construction and Testing of Zinc Finger Nucleases. Nat. Protocols, 1:1329-1341.

Gommans, W.M., McLaughlin, P.M.J, Lindhout, B.I., Segal, D.J., Haisma, H.J, van der Zaal, B.J., & Rots, M.G. (2006) Engineering zinc finger protein transcription factors to down-regulate the epithelial glycoprotein-2 promoter as a novel anti-cancer treatment. Mol. Carcinogenesis, 46:391-401.

Szczepek, M., Brondani, V., Büchel, J., Serrano, L., Segal, D.J. and Cathomen, T. (2007) Structure-based redesign of the dimerization interface reduces the toxicity of zinc finger nucleases. Nat. Biotechnol., 25:786-793.

Porter, J.R., Stains, C.I., Segal, D.J., and Ghosh, I. (2007) A sensitive split beta-lactamase sensor for the sequence specific detection of DNA methylation. Anal. Chem., 79:6702-6708.

Camenisch, T.C., Brilliant, M.H., and Segal, D.J. (2008) Critical parameters for genome editing using zinc finger nucleases. Mini. Rev. Med. Chem., 8:669-676. Review.

Brayer, K.J., and Segal, D.J. (2008) Keep your fingers off my DNA – protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem. Biophys., 50:111-131. Review.

Brayer, K.J., Kulshreshtha, S., and Segal, D.J. (2008) The protein binding potential of C2H2 zinc finger domains. Cell Biochem. Biophys., 51:9-19.

Zykovich, A., Korf, I. and Segal, D.J. (2009) Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res. 37:e151. (PMC2794170)

See: Complete List of Publications

Recent/Current Teaching

PHA 400C, Principles of Pharmacology

BCM 410A, Molecular & Cell Biology

PHA 250, Functional Genomics: From bench to bedside

MCB221A, Physical Biochemistry

FRS 001, Freshman Seminar: Gene therapy: How genes control you and how you can control them.