A transcriptional atlas of gyrification reveals dynamic spatio-temporal gene expression in the developing ferret cortex

Abstract

Gyrification of the cerebral cortex is essential for healthy brain development, and disruptions to this process lead to severe structural and functional abnormalities associated with long-term behavioural and psychiatric consequences. Basal radial glial cells (bRGC), residing in the expanded outer subventricular zone (oSVZ), are thought to drive gyrification. However, the transcriptional programs guiding this process remain poorly defined. We aimed to profile gene expression within the oSVZ of the developing ferret cortex, a species that displays postnatal gyrification, at two key stages of cortical folding, capturing its onset and progression. Discrete regions of the oSVZ were microdissected beneath the coronal gyrus and suprasylvian sulcus at the onset (P5, n = 5) and middle (P15, n = 5) of gyrification in the ferret. We performed RNA sequencing, differential expression analysis with gene ontology and pathway analyses with RT-qPCR validation of candidate genes. The results revealed spatially enriched gene sets associated with progenitor proliferation, self-renewal, and neurogenesis, as well as temporal transcriptional enrichment for axonogenesis and extracellular matrix regulation. RT-qPCR validated spatial and temporal expression differences, confirming consistent trends among some key folding-associated candidate genes. However, some genes (namely SOX9, AJAP1, and SEMA3D) showed inverse expression patterns compared to those detected by RNA-Seq and could not be considered validated. Together, these data define the molecular architecture of gyrification, providing a comprehensive transcriptional atlas of the oSVZ in the developing brain. Our findings advance understanding of how coordinated gene networks shape cortical folding, offering insights into the evolutional expansion of the mammalian brain.