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

ABSTRACT: The correct folding of the cerebral cortex is essential for healthy brain development, and disruptions to this process can result in serious structural and functional abnormalities. While basal radial glia cells (bRGCs) in the expanded outer subventricular zone (oSVZ) are known to contribute to gyrification, the gene regulatory mechanisms driving regional cortical folding remain poorly defined. This study examined differential gene expression within the oSVZ of the developing ferret cortex, focussing on regions prospective of the coronal gyrus (CG) and suprasylvian sulcus (SSS) at the onset (postnatal day 5, n = 5) and middle (postnatal day 15, n = 5) of gyrification. We performed high-throughput, paired-end RNA sequencing on discrete laser capture microdissected oSVZ regions from 50 consecutive brain sections, followed by differential expression analysis, gene ontology, and pathway enrichment using EdgeR and SRplot. The data revealed distinct regional transcriptional signatures enriched for genes involved in progenitor cell proliferation, self-renewal, and neurogenesis, as well as temporal enrichment for axonogenesis and the extracellular matrix (ECM). RT-qPCR validation supported several spatial and temporal differences, confirming consistent expression trends for key candidates (e.g., PI4KB, FOXC1, PRUNE1, and FOXM1) and revealing region- and age-specific dynamics. These data suggest the presence of differential transcriptional profiles within the oSVZ that may guide the formation of gyri and sulci though localised regulation of progenitor behaviour. By identifying and validating molecular candidates involved in early cortical folding, this study enhances our understanding of the mechanisms driving gyrification and provides a framework for investigating the genetic basis of cortical malformations.

ORGANISM(S): Mustela putorius furo

PROVIDER: GSE304435 | GEO | 2026/08/12

REPOSITORIES: GEO

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Project description:Our brains accommodate a largely folded cerebral cortex that associates to our advanced brain functions. Several theories have been proposed to explain the cortical folding process, reasoning the mechanical forces as neuronal tension in underlying layers, cellular expansion and glial progenitor’s diversity in the OSVZ; but the mechanistic insights and underlying genomics changes causing the appearance of cortical folds is still illusive. Importantly, no studies have attempted to comprehensively characterize the gene regulatory networks underlying cortical folding during development. Here, by using ferret as a model system, we have compared the transcriptomes of germinal layers between sulci and gyri, of different cortical areas and across two developmental stages (E30 & E34), to achieve a comprehensive understanding of the spatio-temporal dynamics of gene expression of cortical progenitors. Furthermore, we have also characterized the epigenetic landscape of germinal layers at E30 and E34, a critical period for their development, to correlate changes in chromatin at promoter and enhancer regions with the observed changes in gene expression. Our preliminary results indicate towards a clear transformational axis of gene regulation between germinal layers. By performing motif analysis of differentially expressed gene (DEGs), we reveal transcription factors which might have a critical role in determining cortical folding. The genes targeted by these factors belong to important pathways implicated in proliferation and neurogenesis. We highlight potential candidates in cortical folding through functional validation studies and acetylation (H3K27ac) levels for these genes correlate with their expression state. Importantly, these are critical for cell adhesion, migration and proliferation processes in-line with previous studies stating that proliferative divisions cause neocortical expansions. Our findings will have strong impact on the clinical interventions for neurological disorders relating to cortical malformation, while at the same time enhancing our understanding of molecular circuitry underlying gyrencephalic brain development and folding.

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

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