Research & Initiatives
Ongoing Research:
Manipulating epigenetic mechanisms in neurologic genetic diseases
Angelman syndrome is a rare neurogenetic disease that is the textbook example of imprinting disorder. We are using artificial transcription factors to activate the epigenetically silenced gene in the brain. This project is funded by the Foundation for Angelman Syndrome Therapeutics.
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High-throughput investigations of CRISPR-DNA interactions.
We continue to develop new methodologies for genome editing, such as methods to study the 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.
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Previous research projects:
Functional genomics of noncoding 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 to 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 effects of specific human mutations in the background of millions of other genetic differences between two individuals.
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, TALE, and CRISPR 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 effects of specific human mutations in the background of millions of other genetic differences between two individuals. This work is generously supported by the W.M. Keck Foundation.
Designing permanent inactivators of HIV
We are designing zinc finger, TALE, and CRISPR 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). This work is partly supported by the National Institutes of Health.
A bad day for Malaria
We are designing TALE and CRISPR artificial transcription factors to manipulate genes in the malaria-causing pathogen Plasmodium falciparum. These tools will allow us to learn a lot more about the function of the 5,000 genes, and hopefully lead directly or indirectly to new targeted therapies. This work is supported by the Bill and Melinda Gates Foundation.
Targeting the tumor microenvironment of Neurofibromatosis
We are designing TALE transcription factors that will be able to home in on plexiform neurofibromas in mice and disrupt the tumor microenvironment. Existing data suggests this approach should halt or regress these often untreatable tumors. This work is supported by the Department of Defense.
High-throughput investigations of zinc finger-DNA interactions
We have 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. 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.
