Genome-scale in vivo Perturb-seq profiling of 1,947 disease-associated genes across 7.7 million cells in the mouse brain reveals that genetic perturbations exhibit context-dependent essentiality and organize into modular transcriptional programs, with human neurodevelopmental disease genes producing cell-type-specific effects that converge on synaptic signaling pathways in cortical and subcortical neuronal populations.

Functional genomics studies have provided critical insights into cell type-specific gene regulatory programs, but to date most have been conducted in wild-type tissues or cell cultures. Here, we present a gene expression functional atlas across the mouse brain. We use an enhanced in vivo Perturb-seq platform to analyze transcriptome-wide responses to loss of 1,947 disease-associated genes, profiling over 7.7 million cells spanning major brain regions and neuronal populations. We find striking cell-type-specific essentiality and transcriptional programs and show that closely related disease genes such as two NMDA receptor subunits can drive opposing transcriptional programs. Together, this work reveals insights into the genetics and mechanisms of neurodevelopmental, psychiatric, and neurodegenerative diseases in vivo, paving the way for the design of future genetic medicine.