Restricted (Penn State Only)
Baumann, Douglas G
Graduate Program:
Biochemistry, Microbiology, and Molecular Biology
Doctor of Philosophy
Document Type:
Date of Defense:
February 22, 2018
Committee Members:
  • David Scott Gilmour, Dissertation Advisor
  • David Scott Gilmour, Committee Chair
  • Joseph C. Reese, Committee Member
  • Lu Bai, Committee Member
  • Tae-Hee Lee, Outside Member
  • Shaun A Mahony, Committee Member
  • Promoter
  • Transcription
  • Drosophila
  • Initiation
  • Glutathione
  • Motif 1
  • Pausing
  • GST
  • Housekeeping
  • TRF2
  • TBP-related factors
  • TBP
  • DREF
  • M1BP
  • DRE
  • Motif 6
  • TADs
  • GFZF
Regulation of gene expression is a key driver of organismal development and cellular differentiation. Misregulation of gene expression disrupts development and drives many disease states. While cells modulate gene expression through a variety of processes, transcription is thought to be the most critical and highly regulated process in gene regulation. Ultimately, all transcription regulatory signals converge at the core promoter. Here, I investigate the function of the conserved Drosophila core promoter element Motif 1. Most of our knowledge of transcription initiation comes from studies on promoters with a TATA box and Initiator. While these studies have yielded invaluable information, most promoters lack this combination of elements. Thus, our knowledge of the mechanisms that drive initiation from promoters with different core promoter elements is limited. In order to better understand alternative mechanisms of initiation, I investigated ribosomal protein (RP) gene transcription in Drosophila. I focused on RP genes for several reasons. First, Motif 1 is enriched at RP gene promoters in Drosophila. Second, TBP is not required for transcription of RP genes. Third, in all higher eukaryotes examined, the TCT motif replaces the Initiator sequence at RP gene transcription start sites. Finally, RP genes represent a well-defined gene-regulatory network and are thought to be coordinately expressed. For these reasons, the RP genes offer a compelling model system to study alternative initiation mechanisms and the coordinate transcription of gene networks. Here, I demonstrate that Motif 1 and M1BP are required for RP gene transcription. Additionally, I found that M1BP works at RP genes by recruiting the TBP-related factor 2 (TRF2) to RP gene promoters. My data shows for the first time that TRF2 is recruited to promoters by sequence-specific binding factors. This resolves a long-standing question in the field since TRF2 does not bind DNA in a sequence-specific manner. Furthermore, I show that the largest subunit of the general transcription factor TFIID associates with all RP gene promoters in vivo. Thus, while previous reports called into question TFIID’s role in initiation at TCT motif-containing RP genes, this finding further attests to TFIID’s key role in transcription. I also identify an M1BP interacting protein called GFZF and investigated its function. I show that GFZF is a glutathione S-transferase (GST) and that it is essential for transcription activation. These results provide the first example of a transcription factor with GST activity. GFZF has appeared in a number of genetic screens that implicate it in processes as disparate as hybrid inviability and positive regulation of RAS/MAPK signaling. Because little was known about GFZF’s molecular function, the authors of these reports explained and interpreted GFZF’s appearance in these screens in complex and unclear terms. My findings suggest GFZF’s involvement in these disparate cellular processes results from its association with over 1800 housekeeping gene promoters. Many of these housekeeping genes are directly involved in the processes that were being investigated. The knowledge of GFZF’s molecular and cellular function should guide future interpretations when GFZF appears in large-scale screens. Finally, while it remains unclear why a transcription factor possesses a functional GST domain, I discuss ways that a transcription factor with GST activity might function in gene regulation. This might include roles in the transcriptional response to stress and the maintenance of genome integrity.