In the development of the central nervous system, thousands of neuronal subtypes must be generated, each with their own unique molecular properties. This process is governed by selector transcription factors, which specify cell-identities by binding to cell-type specific genomic regulatory elements. These regulatory elements, dispersed across extragenic regions of the genome, establish precise long-distance interactions with target gene promoters to regulate their expression. While prior studies have emphasized the roles of distally bound selector transcription factors in cell-type specification, the involvement of gene promoters in the regulation of gene expression remains underexplored. In this dissertation, I analyze the role of promoter elements in regulating neuronal gene expression programs using a comprehensive approach that combines high-throughput genomics and targeted experimental manipulations.
In Chapter 2, I reveal a highly flexible regulatory system utilized in the nervous system: neuronal promoters are universal and can thus be activated by any enhancer found within their regulatory neighborhood. This model of promiscuous neuronal promoters raises two important questions: Is promoter promiscuity a universal phenomena? What are the promoter elements that facilitate universality? To address these questions in Chapter 3, I first find that promoters of genes associated with pluripotency exhibit incompatibility with neuronal enhancers. Then, to test what promoter elements encode for this incompatibility, and also which elements endow neuronal promoters with their promiscuity, I developed a novel promoter-screening strategy. Through this work, I discovered novel aspects of enhancer-promoter communication. First, core promoters are universal and can be induced by non-cell identity matched distal enhancers. Second, promoter-proximal regions serve to modulate expression from universal core promoters by either dampening or potentiating their responsiveness to distal enhancers. This work suggests that in addition to distal regulatory elements, promoter-proximal regions also play an active role in fine-tuning cell-type specific gene expression programs by either modulating induction or repressing ectopic expression.
Finally, in Chapter 4, I explore another aspect of the regulation of cell-identity during development, shifting my focus away from selector transcription factors and instead on “secondary” transcription factors induced during differentiation. Here, I utilize a multi-omic approach to characterize the role of Mnx1 in motor neuron development. Analysis of its effects on gene expression, distal genomic binding patterns, and influence on the overall regulatory landscape reveals that Mnx1 plays a role in maintaining the motor neuron cell-identity by ensuring robust expression of motor neuron genes and preventing ectopic expression of genes normally restricted to alternate neuronal subtypes. This suggests that “secondary” transcription factors play a role in refining cellular identities established by selector transcription factors.
Integrating these findings with prior research in central nervous system development underscores that while neuronal gene expression programs are primarily established through the actions of selector transcription factor-bound distal regulatory elements, promoters and secondary transcription factors contribute to the fine-tuning of transcription and, consequently, cell identity.
| Identifer | oai:union.ndltd.org:columbia.edu/oai:academiccommons.columbia.edu:10.7916/yqzg-rr62 |
| Date | January 2023 |
| Creators | Sinha, Abhishek |
| Source Sets | Columbia University |
| Language | English |
| Detected Language | English |
| Type | Theses |
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