Getting to the source: measuring the primary response to acute transcription factor perturbation

Transcription factors (TFs) define and drive cellular identity and state. The coordinate activities of TFs dynamically regulate gene expression physiologically during development and in response to environmental cues. However, transcription is dysregulated in many disease states, including malignancies. Thus it is critical to study the mechanisms by which TFs regulate transcription of their target genes. This dissertation sets out to do so for the TF TRPS1 in a cell line model of luminal breast cancer. Chapter 1 serves as an introduction to breast cancer, the key TFs TRPS1 and estrogen receptor alpha (ER), and the main experimental approach, targeted protein degradation (TPD) to study TF function. Chapter 2 details the methods we use to analyze the data from nascent transcriptional profiling experiments. These methods are most specific to the precision nuclear run-on assay we use, but there are many parallels with the other genome-wide sequencing assays used in the rest of this dissertation. In Chapter 3, we use TPD to demonstrate that acute TRPS1 depletion redistributes ER binding genome-wide, both activating and repressing transcription of genes related to cancer cell fitness. In Chapter 4, we follow up on an initial observation made in the cell lines we generated, that acute TRPS1 depletion in three independent clones activates cholesterol biosynthesis gene transcription. In Chapter 5, I list my contributions to two other published works. Finally, Chapter 6 serves as a discussion of the conclusions drawn from this dissertation and the future directions of this work.