A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex

Xavier, Andre M, Lin, Qianyu, Kang, Chris J, Cheadle, Lucas (June 2024) A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex. bioRxiv. ISSN 2692-8205 (Public Dataset)

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Abstract

Sensory experience drives the refinement and maturation of neural circuits during postnatal brain development through molecular mechanisms that remain to be fully elucidated. One likely mechanism involves the sensory-dependent expression of genes that encode direct mediators of circuit remodeling within developing cells. However, while studies in adult systems have begun to uncover crucial roles for sensory-induced genes in modifying circuit connectivity, the gene programs induced by brain cells in response to sensory experience during development remain to be fully characterized. Here, we present a single-nucleus RNA-sequencing dataset describing the transcriptional responses of cells in mouse visual cortex to sensory deprivation or sensory stimulation during a developmental window when visual input is necessary for circuit refinement. We sequenced 118,529 individual nuclei across sixteen neuronal and non-neuronal cortical cell types isolated from control, sensory deprived, and sensory stimulated mice, identifying 1,268 unique sensory-induced genes within the developing brain. To demonstrate the utility of this resource, we compared the architecture and ontology of sensory-induced gene programs between cell types, annotated transcriptional induction and repression events based upon RNA velocity, and discovered Neurexin and Neuregulin signaling networks that underlie cell-cell interactions via CellChat . We find that excitatory neurons, especially layer 2/3 pyramidal neurons, are highly sensitive to sensory stimulation, and that the sensory-induced genes in these cells are poised to strengthen synapse-to-nucleus crosstalk by heightening protein serine/threonine kinase activity. Altogether, we expect this dataset to significantly broaden our understanding of the molecular mechanisms through which sensory experience shapes neural circuit wiring in the developing brain.

Item Type:	Paper
Subjects:	organism description > animal > mammal > rodent > mouse neurobiology neurobiology > neuroscience
CSHL Authors:	Cheadle, Lucas Kang, Chris Lin, Qianyu Xavier, Andre
Communities:	CSHL labs > Cheadle lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	26 June 2024
Date Deposited:	12 Jul 2024 12:52
Last Modified:	12 Jul 2024 12:52
PMCID:	PMC11230371
Related URLs:	Publisher
Dataset ID:	GEO: GSE269482
URI:	https://repository.cshl.edu/id/eprint/41600

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