EAGER: Rapid Enrichment, Sequencing, and Assembly of Targeted Genomic DNA

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Intellectual Merit: Genes are the fundamental unit of biological information. Most genes are discrete segments of DNA which are "expressed" by being used as the templates for RNA production (a process known as transcription); subsequent decoding of the RNA (a process known as translation) results in the production of a protein with a defined function in the cell. Control of gene expression is critical for all organisms; regulation of the initiation of transcription is a critical step at which gene expression is controlled. Regions of DNA flanking transcribed genes often contain short sequences termed cis-regulatory elements (CREs). CREs are bound by proteins which in turn control initiation of transcription from the neighboring gene; this binding typically requires defined DNA sequences within the CREs. CREs which are important maintain a constant sequence over evolutionary time, while the other DNA surrounding them is unconstrained and drifts in sequence. Thus, a powerful method to identify important CREs is to align DNA sequences flanking transcribed genes from multiple, related species. A major technical bottleneck of this approach is determining the flanking DNA sequences themselves. This project seeks to develop a rapid and flexible method to quickly determine the DNA sequence surrounding a gene of interest in multiple species.Broader Impacts: This project involves the training of a female Ph.D. student, and as such, addresses the need to broaden inclusion of women in the Science, Technology, Engineering, and Mathematics (STEM) fields. The methodology itself has the potential to catalyze the discovery of multiple CREs for critical genes. The resulting understanding of gene regulation may in turn have positive impacts in many areas of the biological sciences, as well as potential practical applications in biotechnology.