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Abstract

Unipolar brush cells (UBC) are excitatory interneurons in the cerebellum that facilitate sensorimotor processing for eye, head, and body position. Its classic morphology is a single short dendritic brush. UBCs are one of three glutamatergic cell types from the rhombic lip. Early in development, these glutamatergic lineages require the transcription factor Pax6—UBCs specifically need Pax6 for proper cell production. Gene regulatory networks (GRNs) model how cells arrive at their observed state—an apt approach for studying developmental trajectory. GRN perturbations are simulated gene expression changes that serve as an in silico discovery tool for genes of interest, and GRNs of specific glutamatergic lineages have not yet been modeled. UBCs are a promising lineage of interest because of Eomes/Tbr2 as its cell specific marker, its two molecularly distinct subtypes, and its key developmental timepoints (E10.5 to P14) are represented in publicly available datasets. The present study creates and perturbs GRNs using scRNA-seq and snATAC-seq data. CellOracle and SCENIC+ are perturbation algorithms that simulate gene of interest in silico knockouts. The in silico knockouts are compared with in-house Pax6-null scRNA-seq data and a curated set of nine developmentally relevant genes (Eomes, Wls, Atoh1, Pax6, Lmx1a, Calb2, Plcb1, Grm1, Plcb4) to evaluate alignment. The pipeline provides the basis for studying other cerebellar cell types through an inference-based developmental model.