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Mechanisms of transcription factor hub formation and function during embryonic development Samantha Fallacaro
- Format:
- Book
- Thesis/Dissertation
- Author/Creator:
- Fallacaro, Samantha, author.
- Language:
- English
- Subjects (All):
- Developmental biology.
- Biophysics.
- Cellular biology.
- Morphology.
- Genetics.
- 0758.
- 0786.
- 0379.
- 0369.
- 0287.
- Local Subjects:
- Developmental biology.
- Biophysics.
- Cellular biology.
- Morphology.
- Genetics.
- 0758.
- 0786.
- 0379.
- 0369.
- 0287.
- Genre:
- Academic theses
- Physical Description:
- 1 online resource (156 pages)
- Contained In:
- Dissertations Abstracts International 87-12B
- Place of Publication:
- Ann Arbor : ProQuest Dissertations and Theses, 2026
- Language Note:
- English
- Summary:
- A fundamental challenge of gene regulation is the requirement for transcription factors (TFs) to navigate a crowded nucleus to locate specific enhancers. Once at a target site, TFs must consistently occupy an enhancer to regulate gene expression despite having very short (~ tens of seconds) residence times on chromatin. The measured high occupancy of TFs at their targets is thought to be driven by increasing binding frequency (on rates) that counteract short individual binding events. The formation of local high-concentration TF clusters, frequently termed "hubs" or "condensates," have been thought to increase TF on-rates by concentrating factors around genomic targets. Clustering is often considered to be non-stochiometric to the number of bindings sites and is proposed to occur through multi-valent protein-protein interactions and driven by thermodynamic phase separation. However, it remains debated whether clusters are autonomous regulatory structures that tune TF binding or if they are simply emergent properties of underlying molecular interaction kinetics. This dissertation presents an analysis on the formation and function of TF hubs using the morphogen TF Dorsal and the pioneer TF Zelda in Drosophila embryos as a model system. To investigate hub formation, I used high-resolution light-sheet microscopy with live imaging of transcription factor kinetics and nascent transcripts. To quantify the biophysical properties of TF hubs, I developed image analysis pipelines in Python to automate 3D hub segmentation and extract kinetic and morphological features in the nucleus and at labeled target sites. These tools enabled the high-fidelity measurement of TF occupancy and transcriptional bursting in vivo. I demonstrate that the apparent biophysical properties of hubs, such as intensity and stability, directly reflect underlying binding kinetics. Specifically, these properties scale predictably with the number of binding motifs and protein on rates at associated enhancers. These findings suggest that the TF search process is not diffusion-limited, and TF occupancy is limited by local binding kinetics. Furthermore, we demonstrate that TF search and binding kinetics is dependent on a kinetic balance between TF-DNA and protein-protein interactions. Together, these results suggest that TF hubs are a manifestation of enhancer occupancy levels rather than regulatory assemblies that promote occupancy
- Notes:
- Source: Dissertations Abstracts International, Volume: 87-12, Section: B.
- Advisors: Mir, Mustafa Committee members: Good, Matthew C.; Lim, Bomyi; Raj, Arjun; Joyce, Eric
- Ph.D. University of Pennsylvania 2026
- Vendor supplied data
- Local Notes:
- School code: 0175
- ISBN:
- 9798247982029
- Access Restriction:
- Restricted for use by site license
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