All ETDs from UAB

Advisory Committee Chair

David A Schneider

Advisory Committee Members

Chad S Hunter

Natalia Y Kedishvili

Elliot J Lefkowitz

Rui Zhao

Document Type


Date of Award


Degree Name by School

Doctor of Philosophy (PhD) Heersink School of Medicine


There are at least three eukaryotic RNA polymerases (Pols), Pols I, II, and III. These Pols are essential for transcription, where RNA is synthesized from various DNA templates. While transcription has been well-studied for decades, there are still many questions that remain unanswered about how this process is regulated for each of the three Pols. Transcription is highly regulated and complex, therefore, many different mechanisms exist to tightly control it in the cell. Some of these mechanisms include regulation by transcription factors and co-transcriptional RNA processing. While these regulatory mechanisms are of great interest, they have not yet been fully characterized. Recently, our lab adapted a novel technique, native elongating transcript sequencing (NET-seq), to probe for Pol I occupancy at single-nucleotide resolution in vivo. Using NET-seq, we investigated the role of a highly conserved transcription factor, Spt4, in transcription by Pol I. We found that Spt4 promotes Pol I processivity during transcription elongation. Additionally, we used NET-seq to determine that a point mutation in the largest subunit of Pol I (rpa190- F1205H) caused alterations to the pause profiles of Pol I throughout the rDNA template and resulted in defects in rRNA processing. These findings suggest that transcription elongation is coupled to rRNA processing, and that this relationship is very sensitive to changes in transcription elongation. Altogether, our studies in this dissertation used a novel technique, NET-seq, to characterize various regulatory mechanisms of transcription by Pol I that were previously not well-defined. This identification of the role of a transcription factor, Spt4, and the tight control between transcription elongation and rRNA processing adds further insight into the complexity of regulatory mechanisms controlling transcription by Pol I.

Available for download on Friday, May 09, 2025