Honors Theses

Date of Award

5-2025

Document Type

Undergraduate Thesis

Degree Name

BS

Department

Biomedical Sciences

Faculty Mentor

Glen Borchert

Advisor(s)

Jeffrey De Meis, Alison Henry

Abstract

Gene regulation is governed by complex networks of interactions between enhancers and promoters, regions of the genome that are typically distant from one another yet functionally linked through chromatin looping. Recent research has revealed the significant role of Gquadruplexes (G4s) in facilitating these interactions. This thesis explores the role of long Gquadruplex regions (LG4s) in enhancer–promoter communication, proposing that these regions mediate physical interactions between enhancers and their target promoters through direct G4:G4 interactions. Using a chromatin conformation capture (EQuIP-seq), electrophoretic mobility shift assays (EMSA), and luciferase reporter assays, the study demonstrates that LG4s may drive gene expression by promoting the formation of stable enhancer–promoter loops independent of protein factors. In addition to functional insights, the evolutionary conservation of LG4s across multiple species was examined, revealing that these G4-rich regions are highly conserved. Crossspecies conservation analyses, including comparisons between human, mouse, and other vertebrates, underscore the fundamental role of G4-mediated enhancer–promoter interactions in maintaining gene regulatory networks throughout evolution. This conservation suggests that G4- mediated regulation is not a species-specific phenomenon, but rather a conserved mechanism across eukaryotic organisms, essential for coordinating gene expression in diverse biological contexts. These findings provide a novel perspective on the evolution of gene regulation, highlighting the role of DNA structural motifs like G4s in shaping the architecture of the genome.

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© 2025 Shahem Alqudah ALL RIGHTS RESERVED

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