Degree
Doctor of Philosophy (PhD)
Department
Biological Sciences
Document Type
Dissertation
Abstract
Enhancer-promoter communication regulates spatiotemporal gene expression fundamental to the development of metazoans and the cell-lineage-specific transcriptional responses to extrinsic signals. These interactions can occur over large distances. However, it remains unclear how enhancer-promoter specificity is established. Several mechanisms have been proposed, including dividing chromosomes into chromatin domains separated by insulator elements that limit enhancer-promoter interactions to their resident domains. These domains can be seen as topologically associating domains, or TADs, by methods such as Hi-C. The insulator-binding protein BEAF-32 is the most predominant DNA-binding protein at Drosophila TAD boundaries. These inter-TAD regions contain active housekeeping genes. Consistent with this, BEAF-32 usually binds near transcription start sites of housekeeping genes. This raises the question of whether BEAF-32 plays a role in gene activation in addition to having an insulator activity. We approached the question in two ways. First, we sought to identify transcription-associated proteins that BEAF-32 directly interacts with. We investigated direct physical interactions and how common it is for these interactions to reflect an ability to communicate from a distance with BEAF-32, focusing on potential interacting partners FACT histone chaperone subunits Dre4 and SSRP and transcription factors DREF, Rib, and ROW. We provide evidence of BEAF-32 direct interaction with these proteins and show it can loop with SSRP and ROW. Second, we investigated BEAF-32 preference for housekeeping promoters over regulated promoters in its promoter activity. We interrogated fifteen housekeeping promoters plus four mutant variants, and fourteen regulated promoters plus four DSCP (Drosophila synthetic core promoter) derivatives. BEAF-32 activates all the housekeeping promoters assessed and certain regulated promoters containing only Inr. Two promoters lacking known motifs were also activated. Regulated promoters containing TATA-box, Inr-MTE, Inr-DPE, and Inr-MTE-DPE were not activated. Importantly, our data suggests that BEAF-32 is not just involved in helping to specify domain boundaries, but also is directly involved in regulating gene expression.
Date
1-10-2025
Recommended Citation
Negedu, Sunday, "Beyond Chromatin Insulator Function: Analysis of Drosophila BEAF-32 Activation of Core Promoters and Its Interaction with Transcription-Associated Factors" (2025). LSU Doctoral Dissertations. 6669.
https://repository.lsu.edu/gradschool_dissertations/6669
Committee Chair
Hart, Craig
Included in
Biochemistry Commons, Cell Biology Commons, Molecular Biology Commons, Molecular Genetics Commons
