Identification of DNA Regulatory Elements Active in Chronic Intestinal Inflammation Using FAIRE-seq (2015)

Undergraduates: Julia Whitley, Vishal Iyer Maren Cannon, Matthew Weiser Gregory Gipson, Jeremy Simon, Eric Lee, Shehzad Sheikh

Faculty Advisor: Shehzad Sheikh
Department: Biology

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The inflammatory bowel diseases (IBD) are a group of chronic inflammatory conditions that affect the gastrointestinal tract. IBD affects between 1 and 2 million Americans, and there is no cure. Several genetic variants (SNPs) have been linked to IBD, but it is unknown which of these variants are causative. The majority of disease-associated variants occur in regions of the genome that do not code for proteins, suggesting that these SNPs play a role in gene regulation. I tested the potential regulatory function of the IBD-associated SNP rs10896788. This variant was cloned into a liver cell line and analyzed using a luciferase reporter assay. When compared to the non-risk allele, the variant displayed an increase in gene expression. These results suggest that this variant may act as a regulatory element that increases gene expression. Understanding the function of IBD-associated SNPs may elucidate the role of genetic variation in IBD pathogenesis.