David Segal, Ph.D.
- Gene and epigene editing to treat neurologic disease.
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 zinc finger, TALE, and CRISPR/Cas nucleases and transcription factors.
- Manipulating epigenetic mechanisms in neurologic genetic diseases
Angelman syndromes is a rare neurogenetic disease that is the textbook examples of imprinting disorder. We are using artificial transcription factors to activate the epigenetically silenced gene in in the brain. This project is funded by the Foundation for Angelman Syndrome Therapeutics..
- Functional genomics of non-coding elements
In collaboration with Peggy Farnham and the ENCODE consortium, we are using targetable nucleases and transcription factors based on zinc fingers, Transcription Activator-like Effector (TALE), and Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) to disrupt non-coding genetic elements in the human genome to better understand their function. Our most recent efforts focus on creating epigenomic editing tools that can precisely manipulate epigenetic information at specific loci. Such tools can be used for the long-term control of gene expression for both research and therapeutic applications.
- Genetic variation in health and disease
Several genetic variations (SNPs) have been associated with an increased risk of common complex disorders, such as colorectal cancer. In collaboration with Luis Carvajal-Carmona, we are using targetable nucleases identify causative SNPs and determine their mechanism of function. Our most recent efforts focus on creating tools that can precisely alter a single base pair at specific loci. 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.
- High-throughput investigations of CRISPR-DNA interactions
We continue to develop new methodologies for genome editing, such as methods to study off-target activity of CRISPRs and factors for targeted epigenetic modification. We employ methods of directed evolution for protein engineering and ChIP-seq and RNA-seq to examine the effects of tools on a genome-wide scale.
Graduate Group Affiliations
O'Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, Mackay JP, Farnham PJ, and Segal DJ. (2017) dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nucleic Acids Res, in press. DOI: 10.1093/nar/gkx578.
Fink KD, Deng P, Gutierrez J, Anderson JS, Torrest A, Komarla A., Kalomoiris S, Cary W, Anderson JD, Gruenloh W, Duffy A, Tempkin T, Wheelock V, Segal DJ, and Nolta, JA. (2016) Allele-specific reduction of the mutant huntingtin allele using transcription activator-like effectors in human Huntington’s disease fibroblasts. Cell Transplant. 25:677-686.
Bailus, B.J., Pyles, B., McAlister, M.M., O’Geen, H., Lockwood, S.H., Adams, A.A., Trang Nguyen J.T., Berman R.F., and Segal, D.J. (2016) Protein Delivery of an Artificial Transcription Factor Restores Widespread Ube3a Expression in an Angelman Syndrome Mouse Brain. Mol Ther. 24:548-555.
O'Geen, H., Henry, I.M., Bhakta, M.S., Meckler, J.F., Segal, D.J. (2015) A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res. 43:3389-3404.
Johnson, L.M., Du, J., Hale, C.J., Bischof, S, Feng, S., Chodavarapu, R.K., Zhong, X., Marson, G., Pellegrini, M., Segal, D.J., Patel, D.J., Jacobsen, S.E. (2014) SRA/SET domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature, 507:124-128.
Owens, J.B., Mauro, D., Stoytchev, I., Bhakta, M.S., Kim, M.-S., Segal, D.J. and Moisyadi, S. (2013) Transcription activator like effector (TALE) directed piggyBac transposition in human cells. Nucleic Acids Res, 41:9197-9207. (PMID: 23921635)
Mackay, J.P., Segal, D.J., and Crossley, M. (2013) Is there a telltale RH fingerprint in zinc fingers that recognize methylated CpG dinucleotides? Trends Biochem Sci, 38:423.
Segal, D.J. and Meckler, J.F., (2013) Genome Engineering at the Dawn of the Golden Age, Annu. Rev. Genomics Hum. Genet, 14:135–158.
Meckler, J.F., Bhakta, M.S., Kim, M-S., Ovadia, R., Habrian, C.H., Zykovich, A., Yu, A., Lockwood, S.H., Morbitzer, R., Elsäesser, J., Lahaye, T., Segal, D.J., and Baldwin, E.P. (2013) Quantitative Analysis of TALE-DNA Interactions Suggests Polarity Effects, Nucleic Acids Res, 41:4118-4128.
Bhakta, M.S., Henry, I.M., Ousterout, D.G., Theva Das, K., Lockwood, S.H., Meckler, J.F., Wallen, M.C., Zykovich, A., Yu, Y., Leo, H., Xu, L., Gersbach, C.A. and Segal, D.J. (2013) Highly Active Zinc-Finger Nucleases by Extended Modular Assembly, Genome Research, 23:530-538.
Meier, J.L., Yu, A., Korf, I., Segal, D.J. and Dervan, P.B. (2012) Guiding the Design of Synthetic DNA-Binding Molecules with Massively Parallel Sequencing, J Am Chem Soc. 134:17814-17822.
Owens, J.B., Urschitz, J., Stoytchev, I., Dang, N.C., Stoytcheva, Z., Belcaid, M., Maragathavally, K.I., Coates, C.J., Segal, D.J., and Moisyadi, S. (2012) Chimeric piggyBac Transposases for Genomic Targeting in Human Cells. Nucleic Acids Res, 40:6978-6991.
Mackay, J.P., Font, J., and Segal, D.J. (2011) The prospects for designer single-stranded RNA-binding proteins. Nature Struct Mol Biol, 18:256-261 .
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)
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.
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.
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.
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.
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.
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.
Carroll, D., Morton, J.J., Beumer, K.J. & Segal, D.J. (2006) Construction and Testing of Zinc Finger Nucleases. Nat. Protocols, 1:1329-1341.
- GGG 201A,Advanced Genetic Analysis
- FRS 001, Genomics and Gene Therapy: How Genes Control You and How You Can Control Them
- MCB 211, Physical Biochemistry - DNA section
- PHA 225, Gene Therapy
- PHA 250, Functional Genomics: from Bench to Bedside