The sequencing of the human genome in 2001 was a milestone for science. However, the origins of most diseases and developmental processes remain obscure. It is now clear that beyond the genetic code there is a wealth of information stored in the dynamic organization of nuclear structures. This “epi-genetic” information controls how genes are accessed and expressed and is often misregulated in disease; yet, so far there have been few ways to synthetically read, write, and engineer it.
Drawing upon interdisciplinary approaches in engineering, biology, and physics our lab develops molecular technologies to expand and unlock new ways to control, understand, and harness chromatin. These technologies will enable researchers and engineers to manipulate features of chromatin, such as it’s biochemistry and 3-dimensional structure, in highly defined and specific ways. These technologies can be used to reveal the mechanisms of developmental transitions and diseases. In addition, they can be exploited to create synthetic “biological circuits” useful in applications such as antibody production and cancer-killing cells. Epigenetic control is a fundamental and ubiquitous aspect of cell biology; the ability to control its properties will unlock discovery and therapeutic opportunities in many areas of biology, medicine, and biotechnology.
Focus Areas – Synthetic Biology, Neural and Stem Cell Engineering, Bioengineering
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- A molecular assessment of the practical potential of DNA-based computation , CURRENT OPINION IN BIOTECHNOLOGY (2023)
- Chaetocin disrupts the SUV39H1-HP1 interaction independent of SUV39H1 methyltransferase activity , BIOCHEMICAL JOURNAL (2023)
- Profiling transcriptomic responses of human stem cell-derived medium spiny neuron-like cells to exogenous phasic and tonic neurotransmitters , MOLECULAR AND CELLULAR NEUROSCIENCE (2023)
- DINOS: Data INspired Oligo Synthesis for DNA Data Storage , ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS (2022)
- Human Pluripotent Stem Cell-Derived Medium Spiny Neuron-like Cells Exhibit Gene Desensitization , CELLS (2022)
- Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity , INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)
- DNA stability: a central design consideration for DNA data storage systems , NATURE COMMUNICATIONS (2021)
- Effects of early geometric confinement on the transcriptomic profile of human cerebral organoids , BMC BIOTECHNOLOGY (2021)
- Evaluation of UBE3A antibodies in mice and human cerebral organoids , SCIENTIFIC REPORTS (2021)
- Mapping the dynamic transfer functions of eukaryotic gene regulation , CELL SYSTEMS (2021)
This proposal seeks to engineer new experimental platforms for chromatin biology.
This is a fellowship proposal to enable the PI to pivot research directions to obtain new knowledge and expertise to enrich his research program.
Digital information is being generated in excess of 1 zettabyte (1021 bytes) per year worldwide. Existing information storage technologies are reaching major limitations in keeping pace. These limitations include unsustainable increases in the demand for: information capacity, physical storage space, raw materials, and energy to cool and maintain storage systems. DNA, a natural medium of information storage in biological systems, has garnered excitement and attention from both academic and industry groups as a potential next generation storage technology. DNA offers several advantages including a raw capacity of 1 zettabyte per 1 cubic centimeter. In comparison, state of the art electronic storage media would require 1000 cubic meters to store the same information. DNA also exhibits exceptional stability with a half-life of over a hundred years at ambient temperatures and requires minimal energy to maintain. Thus, DNA could be a transformative information storage medium. This project considers the design of a DNA-based data storage system from a thermodynamics perspective, allowing us to fine-tune interactions between DNA strands to achieve high capacity, random access, and search.
There is substantial evidence that chromatin (genomic DNA and the proteins, RNAs, and chemical motifs bound to it) is a central regulator of diverse cellular and disease processes, in particular through its regulation of gene expression. Despite the wide-spread acceptance of its importance and relevance throughout biology, it is remarkable that our understanding of chromatinÃƒÂ¢Ã¢â€šÂ¬Ã¢â€žÂ¢s mechanisms and functions remains very limited and reliant on largely correlative observations or non-specific genome-wide perturbations. Here we propose the engineering of two synergistic and parallel sets of tools. One set of tools will sense and report on the dynamic biochemical and conformational states of chromatin in living mammalian cells. The other set of tools will dynamically induce changes in or ÃƒÂ¢Ã¢â€šÂ¬Ã…â€œeditÃƒÂ¢Ã¢â€šÂ¬Ã‚Â chromatin biochemistry and conformation at specific user-defined genomic loci. The project is organized into the development of chromatin sensors and editors at two spatial scales: 1) the kilobase scale where we tackle biological questions relevant to the dynamic changes in chromatin biochemistry; 2) the megabase scale where we investigate the potential utility of artificial topologically associated domains as a means to efficient and inducibly regulate large numbers of mammalian genes.
This proposal will develop new systems for practical DNA-based information storage systems.
The work combines optogenetics and single cell methods to analyze TF dynamics.
This model will develop human in vitro models of brain circuits.
Angelman syndrome (AS) is a neurological disorder characterized by delayed development, intellectual disability, speech impairment, and ataxia1. The primary molecular driver defining AS is the loss of UBE3A protein in neurons, deriving from either mutation or deletion of maternal UBE3A, as the paternal allele is silenced in neurons. There have been exciting advances in identifying and developing potential therapeutics for Angelman Syndrome. In particular, a leading strategy has been to develop therapeutics that reactivate the paternal copy of UBE3A or that introduce an ectopic copy of UBE3A, with several exciting candidates in preclinical and clinical development. Despite these advances, important challenges remain: Challenge 1. It remains unclear the extent to which rescuing UBE3A expression in adults, children, or even infants will ameliorate the symptoms of AS. Challenge 2. High throughput experimental models for screening and validating therapeutics are currently unable to capture functional readouts at scale. Challenge 3. The human brain exhibits considerable and distinct genetic, cellular, and functional diversity between human genotypes and with rodent models. Challenge 4. Experimental models are needed that better mimic the human in vivo microenvironment. The primary goal of this proposed work is to develop a robust and scalable array of human organoids with embedded microelectrodes that can longitudinally track catecholamine and action potential changes over weeks to months, for downstream applications in drug screening.
This project will engineer sensors of DNA methylation.
This proposal will generate human cell lines to advance our understanding and treatment of ICD and UPD genotypes of Angelman Syndrome.