Electronic Thesis and Dissertation Repository

Thesis Format

Monograph

Degree

Master of Science

Program

Biology

Supervisor

Percival-Smith, Anthony

Abstract

Phenotypic non-specificity is the redundant rescue of a transcription factor (TF) phenotype by multiple distinct TFs. The TF Apterous (AP), expressed in Drosophila melanogaster wing imaginal discs, is required for wing development. Expression of the AP (resident) TF, and three TFs not normally expressed in the same pattern as AP (non-resident TFs), from Upstream Activation Sequence (UAS) transgenes rescue the apnull phenotype. The female-specific DSX TF, DSXF, induces female-like abdominal pigmentation. Expression of DSXF and four non-resident TFs from UAS transgenes rescue female pigmentation. As all these TFs recognize distinct DNA-binding sites, I determined what genes were regulated by the resident and the non-resident TFs. RNA-seq analysis of dissected wing discs and abdomens was performed. Sets of regulated genes showed extensive coregulation for rescue of both phenotypes. Results determined the mechanism of TF function and gene regulation to explain phenotypic non-specificity which has broader implications for current gene expression models.

Summary for Lay Audience

Transcription is the process that transforms the information stored in DNA into a mRNA copy. This process begins when RNA polymerase (RNAP), the protein that performs the copying, binds to a gene’s promoter, a specific sequence at the beginning of a gene. Transcription factors (TFs) are proteins that can either inhibit RNAP from binding, preventing transcription, or help recruit RNAP, enabling transcription. Traditionally, TFs are believed to bind to unique DNA sequences, thus regulating specific genes to produce particular traits. This common understanding of TF function is mainly based on studies in one-celled organisms, like bacteria and yeast, which have fewer genes than more complex organisms like fruit flies and humans. In my research, I explore a different phenomenon called ‘phenotypic non-specificity’, which suggests that a TF’s function can be substituted by other TFs, even if they are not typically required for the phenotype (the observable trait). Previous studies in fruit flies (Drosophila melanogaster) showed that expression by the TFs Apterous (AP), which is required for wing development, and Doublesex (DSX), which is required for sexual development, can be rescued by other TFs that are not normally required for generating these phenotypes or that even bind to the same DNA sequences. The goal of my thesis was to investigate how different TFs can substitute for the TFs normally responsible for these traits. By analyzing RNA sequencing data, I determined which genes are differentially expressed due to expression of the original TF (AP or DSX) and the rescuing TFs by comparing the genes expressed to a control lacking the original TF. The results showed that these rescuing TFs often regulate a similar set of genes in a coordinated manner which may be why they can rescue the phenotype. These findings suggest that in complex organisms, TFs may work together rather than acting alone, redefining how we understand transcription initiation. This research encourages further investigation into the role of redundant TF function and its impact on gene expression and evolution.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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