Investigating the Gene Regulatory Networks Linking Neuronal Identity Specification and Differentiation

Abstract

Neuronal diversity emerges from the spatial and temporal patterning of neural stem cells by various signaling molecules and transcription factors (TFs). This diversity is subsequently established and maintained by another set of TFs called terminal selectors. In the Drosophila optic lobe, these progenitor patterning factors and the unique terminal selector combinations in post-mitotic neurons have been comprehensively described. To understand how information is relayed between these two regulatory programs, we studied Tm2 and Tm6 neurons, with a focus on SoxNeuro, a highly important neurodevelopmental factor. We find that Tm6 terminal selector SoxN is also detectable but not required in Tm2 neurons. We showed that Erm, a candidate terminal selector for Tm1 neurons, a related type, cannot be detected within them and upon its knockdown, no phenotypic changes are observed. We leveraged a simultaneously performed scRNA and ATAC-seq (multiome) dataset to find differentially accessible enhancers of SoxN and generate a reporter line for a candidate enhancer in Tm6. We find that while it does not label cell types of interest and labels non-target cells, it works differently based upon its directionality. Finally, we studied the role of temporal TFs (tTFs), Esg and Ey, in regulating SoxN in Tm1/2/4/6 neurons during neurogenesis and found that Esg overexpression does not affect the normal patterning of these neurons but Ey, that is known to stop the production of Tm2/6, leads to the production of more Tm4 neurons specifically. Overall, the interface of fate specification and identity differentiation is a complex program that resolves developmental history into unique neuronal identities, understanding which can unlock potential for selectively generating and designing neurons to achieve therapeutic ends.