In vivo regulation of progenitor genome organization and cellular diversity

A fundamental question in brain development is how a small group of neural progenitors use a single genome template to generate the vast diversity of neurons that underlie cognitive and motor function. It is generally thought that the three dimensional packaging of the genome underlies cell type specific gene expression. Thus, the physical organization of genes within nuclei must be specific to cell type and developmental stage. While much progress has been made with high throughput approaches to uncovering genome-wide organizational principles at different scales, what level of organization relates to gene function remains largely unknown. These questions are particularly challenging for neural progenitors, which can produce distinct neuronal subtypes over time. First, obtaining cell type and stage-specific genome profiling data that would allow one to detect meaningful organizational features is technically difficult, and such features would be lost by averaging among bulk heterogeneous cell populations. Second, there is a dearth of known trans-acting regulators of genome organization that can be used for gain/loss of function studies to test their impact on genome organization. Third, there are few experimental platforms in which to manipulate genome organization and validate their functional significance on downstream gene expression in vivo. Here, we have established the Drosophila neuroblast (NB, fly neural progenitors) system as an in vivo model to investigate how neural progenitor genome organization impacts its ability to produce distinct transcription programs in the descendent neuronal progeny. We previously showed that the hunchback (hb) gene, a key molecular signature of early-born neurons, relocates to the NB nuclear periphery, where it becomes heritably silenced and refractory to activation in the postmitotic neurons. Thus, changes in the genome organization of the NB progenitor directly regulates competence of the postmitotic progeny to transcribe hb. We discovered 250bp cis-acting element with the hb gene that is necessary and sufficient for hb gene relocation to the NB nuclear lamina, and mapped similar sequences genome-wide. Further, we have identified a trans-acting factor that regulates hb gene relocation and NB competence via its liquid-like, condensate forming properties. Here we will combine genetic and high throughput studies on purified, stage- specific NBs to test how genome dynamics are regulated in neural progenitors in vivo. We will then test the transcriptional consequence of genome reorganization of the NB on gene expression of the descendent neuron. Together, our proposed studies will provide mechanistic insights into how genome organization is regulated in neural progenitors and how genome dynamics contributes to neuronal diversification. Project Number: 1R01HD119838-01 | Fiscal Year: 2025 | NIH Institute/Center: Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) | Principal Investigator: Minoree Kohwi | Institution: COLUMBIA UNIVERSITY HEALTH SCIENCES, NEW YORK, NY | Award Amount: $638,625 | Activity Code: R01 | Study Section: Development - 2 Study Section[DEV2] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R01HD11983801