Impact of guanine quadruplex formation on transcription and open chromatin regions

DNA transcription is impacted by many regulatory inputs intrinsic and extrinsic to DNA sequence itself¹. One such regulation occurs through quadruplexes, also known as G4s. These are a family of alternative nucleic acid structures that are a core of stacked G-quartets (planar arrangement of four guanine bases) ². G4s have high structural stability under physiological conditions and affect transcription regulation, replication, and genomic stability². A variety of tools have been developed to find sequences where G4s could likely develop and cause transcriptional changes. In this study, we use G4Hunter, a computational program, to identify regions where quadruplexes could form within specified genomic areas. Specifically, we used G4Hunter to predict quadruplex formation in promoter regions of genes whose expression and/or chromatin accessibility were significantly altered in bone-marrow derived macrophages (BMDMs) from the IL10KO colitis-prone mouse model upon stimulation by lipopolysaccharide (LPS), a bacterial-derived compound. This was completed to understand connections between changes in chromatin accessibility and gene expression in macrophages, which are key immune cells involved in intestinal inflammation, and how, or if, these changes are related to quadruplex formation.Bachelor of Scienc