Research Symposium

BIO

Hi! My name is Becca Sayad. I am a current biology student in the FSU Honors Program. I am originally from Tampa, FL. My research interests are in genetics and molecular biology. After I graduate from Florida State University, I plan to attend medical school and become a physician.

Investigating the Functional Association of Genes Sharing Cis-Acting Motifs in Maize Using Bioinformatics and Gene Ontology Analysis

Abstract

The research hypothesis is that genes sharing cis-regulatory elements also share biological functions. In maize (Zea mays), hundreds of DNA motifs exist, but their functions remain unknown. To test our hypothesis, we (1) intersected DNA motif families with genes to create gene lists and (2) performed Gene Ontology (GO) analysis using AgriGO. GO terms, such as "development" or "disease response," suggest biological pathways.

This research is crucial because motifs may identify genes responding to similar signals and environmental cues. We selected a motif family with at least 1,000 locations, obtained genomic coordinates as BED files, and used DeepTools Intersect to generate motif-specific gene lists. Our preliminary GO analysis revealed enrichment in specific pathways. For example, genes associated with the motif family "dym63" were enriched for **cellular response to stimulus** (GO:0051716, p = 2.40E-45), **reproductive process** (GO:0022414, p = 1.30E-40), and **organelle organization** (GO:0006996, p = 3.20E-35). The reproductive process category aligns with the motif's origin in developing earshoot, a reproductive tissue.

Some GO terms appear too frequently, suggesting potential false positives. To refine our results, we are developing an independent test for significance. Ultimately, this study will clarify how gene motifs regulate biological pathways, informing genetic strategies for crop improvement.

Keywords: genetics, maize, DNA motif, gene ontology, bioinformatics