Coordinated control of neuronal differentiation and wiring by a sustained code of transcription factors

Abstract

The enormous diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of ∼10 transcription factors that are continuously expressed by them. We show that targeted modifications of this ‘selector’ code induce predictable conversions of cell fates between neurons in vivo. These conversions appear morphologically and transcriptionally complete, arguing for a conserved gene regulatory program that jointly instructs both the type-specific development and the terminal features of neurons. Cis-regulatory sequence analysis of open chromatin links one of these selectors to an upstream patterning gene in stem cells that specifies neuronal fates. Experimentally validated network models show that selectors interact with ecdysone signaling to regulate downstream effectors controlling brain wiring. Our results provide a generalizable framework of how specific fates are initiated and maintained in postmitotic neurons.

Neuronal identity control at the resolution of a single transcription factor isoform

“…See Methods for more details. (d) Expression levels of LPLC2-specific transcription factors (Kurmangaliyev et al, 2020;Ozel et al, 2022) nuclear GFP reporter, and two genes enriched in ectopic, non-LPLC2, clusters (X4/X5).…”

“…Terminal selector genes are thought to establish the terminal characteristics that define final cell identities (Hobert, 2008;Hobert, 2016). Final identity often requires a unique combinatorial expression of terminal selectors to implement all terminal characteristics (Allan & Thor, 2015;Hobert, 2016;Ozel et al, 2022). In this work, we elucidate one gene, broad, that is able to act as a terminal selector to differentiate neuronal identity between LPLC1 and LPLC2 cells through morphological, transcriptomic, and functional connectivity changes.…”

“…The copyright holder for this preprint this version posted June 14, 2024. ; https://doi.org/10.1101/2024.06.14.598883 doi: bioRxiv preprint whole-cell electrophysiology, enabling the functional consequences of perturbations to be evaluated (von Reyn et al, 2014;von Reyn et al, 2017). And perhaps most critically, recent advancements within the field of transcriptomics allow tracking of genetic expression in a celltype-specific manner over the course of development, elucidating the temporal expression profile of specific genes (Davis et al, 2020;Konstantinides et al, 2018;Kurmangaliyev et al, 2020;Ozel et al, 2022;Ozel et al, 2021).…”

Transcriptional complexity in the insect central complex: single nuclei RNA sequencing of adult brain neurons derived from type 2 neuroblasts

“…Neuronal diversity is essential for the proper assembly and function of the adult brain, yet the “parts list” of different neuronal and glial cell types remains incomplete. In Drosophila , the laterally-positioned optic lobes have been well characterized for transcriptionally distinct neurons (Konstantinides et al, 2018; Konstantinides et al, 2022; Özel et al, 2022), but less is known about the central brain, with a whole brain transcriptome (Davie et al, 2018; Li et al, 2022) and a central brain transcriptome reported (Croset et al, 2018).…”

Single cell RNA-seq analysis reveals temporally-regulated and quiescence-regulated gene expression in Drosophila larval neuroblasts

“…In Drosophila, neuronal scRNA-seq has been done on adult brain [12][13][14][15][16], pupae [17][18][19][20][21][22], larvae [23][24][25], and blastoderm-stage embryos [26]. These experiments have provided valuable insight into the number of distinct neuronal types and identified gene candidates for regulating neural subtype function or connectivity.…”