Abstract:

Precise regulation of gene expression is essential for controlling developmental programs, maintaining cellular identity, and ensuring proper tissue function. Dynamic interactions between proteins and cis-regulatory elements integrate molecular mechanisms and extracellular signaling to achieve precise control of transcriptional activity. In this thesis, I investigate protein-DNA-mediated transcriptional regulation across two distinct developmental systems: mouse embryonic stem cells (mESCs) and early Drosophila embryos.

Using PP7/PCP live-cell imaging, I tracked Sox2 transcriptional activity in single mESCs under LIF pathway perturbations (Chapter 2). Removing LIF ligand or inhibiting JAK signaling induced heterogeneous changes in Sox 2 activity, reducing the number of Sox2-active cells. Transcriptional output in remaining Sox2-active cells decreased, caused by smaller and less frequent transcriptional bursts. LIF perturbation also decreased the number of pluripotent cells, with pluripotent marker-positive cells showing higher Sox2 mRNA production. Moreover, Sox2 transcription displayed transcriptional memory, with active mother cells more likely to reactivate Sox2 in daughter cells, even under signaling disruption. These findings reveal quantitative aspects of Sox2 regulation essential for pluripotency maintenance.

In early Drosophila embryos, I investigated how the dosage of the transcription factor Dorsal (Dl) and TF binding sites affinity govern the spatial and temporal regulation of the snail (sna) gene (Chapter 3). Surprisingly, reducing the level of Dl, normally an activator of sna, led to increased sna transcriptional activity. This inverted dosage effect is mediated by the autoregulation of the Sna repressor. Reduced Dl initially decreases Sna protein production, which in turn reduces autorepressive feedback on the sna gene, leading to compensatory increases in sna transcription. Increasing Dl binding sites affinity within sna enhancers also reduced sna transcriptional activity and altered bursting behavior. Finally, we showed that Sna-mediated autorepression modulates enhancer responsiveness in a dosage- and context-dependent manner.

Together, this work reveals how transcriptional feedback mechanisms can modulate gene expression outputs beyond the direct effects of TF input levels. Together, these studies demonstrate how examining gene regulatory dynamics across distinct biological systems can uncover fundamental principles of transcriptional control and inform strategies for targeted modulation of gene expression in biomedical research.

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