CAREER: Exploring nucleosome-depleted sequences for novel applications in synthetic biology

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Fully understanding how chromosomes affect cell behavior is important to many applications in biotechnology and improving human health. Many DNA segments that were previously thought to be just filler, or "junk" DNA, have recently been discovered to influence the cell metabolism in important ways. This project will study the influence of a specific subgroup of these segments on cell behavior. In addition, the principal investigator will develop a uniquely-structured undergraduate research program. She will also mentor next-generation STEM (science, technology, engineering and mathematics) teachers, and promote the participation of underrepresented minorities and persons with disabilities in STEM fields. When completed, this project will have developed new molecular tools for harnessing the power of biological systems to produce important products, and helped encourage and prepare highly-skilled students with diverse backgrounds to engage in STEM careers. This proposal addresses the low orthogonality that is frequently encountered between well-characterized biological components and genetic contexts. The canonical Design-Build-Test-Learn cycle dissects natural complex biological subjects into distinct functional parts through a "subtraction" hierarchy. However, the interplay among multiple layers in new combinations brings about unwanted design imprecision. Selecting three distinct yeast species as testbeds, the principal investigator will systematically characterize the highly exposed nucleosome-depleted genomic regions and create synthetic insulators to counteract genetic context influence on heterologous gene and pathway expression. The concept of insulating transcriptional elements to create designed regions that regulate gene expression with high orthogonality has been applied with some success in bacterial genetic circuits. Efforts in yeast systems, with a higher degree of complexity, are very limited. The highly exposed nucleosome-depleted regions will be further exploited to address lack of stable episomal plasmids faced by many nonconventional yeasts.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.