Molecular diversity of auditory critical period plasticity revealed by single-nucleus RNA sequencing

Auditory experience drives neural circuit refinement during auditory circuit development, but little is known about the genetic regulation of this developmental process. The primary auditory cortex (A1) exhibits a critical period for thalamocortical connectivity between postnatal days P12 and P15, during which tone exposure alters the tonotopic topography of A1. We hypothesized that a coordinated, multicellular transcriptional program governs this window for patterning of the auditory cortex. To test this idea, we generated a multicellular map of gene expression by performing droplet-based, single-nucleus RNA sequencing (snRNA-seq) of A1 across three developmental time points spanning the tonotopic critical period (P10, P15, P20). We also tone-reared mice (7 kHz pips) during the 3-day critical period and carried out snRNA-seq of A1 at P15 and P20. Using semi-supervised clustering and marker genes, we identified and profiled neuronal (glutamatergic and GABAergic) and non-neuronal (oligodendrocytes, microglia, astrocytes, and endothelial) cell types in A1 under these different conditions to identify candidate genes that might regulate auditory critical period plasticity. By comparing normally reared and tone-reared mice, we identified hundreds of genes in both glutamatergic and GABAergic cells with altered expression as a result of sensory manipulation in the critical period. In addition, we identified previously unknown effects of developmental tone exposure on interneuron developmental trajectories. This single-cell transcriptomic resource of the developing auditory cortex will provide a powerful discovery platform for future characterization of mediators of tonotopic plasticity. Five conditions, each with two bioreplicates: P10 normally reared, P15 normally reared, P15 tone reared, P20 normally reared, P20 tone reared.