H3 Acetylation-Induced Basal Progenitor Generation and Neocortex Expansion Depends on the Transcription Factor Pax6

Simple Summary The mammalian cerebral cortex is believed to have gained complexity partly because of the abundance of specific cell types, collectively called basal progenitors. If these cells are deficient in the developing brain, it can lead to cortical structure anomalies, which have implications for defective brain function. Certain regulatory molecules have been found to control the production of basal progenitors during brain development. Key amongst them is the Paired Box 6 (Pax6) transcription factor and a chromatin modification mark called histone 3 lysine 9 acetylation (H3K9ac). However, our knowledge of how these regulatory factors interact to drive the generation of basal progenitors is insufficient. In this current work, we found that the enzyme involved in the acetylation of histone 3 at the 9th lysine interacts with Pax6 at the loci of genes critical for the production and amplification of the basal progenitor cell pool. As such, when both factors are decoupled or downregulated, it leads to depletion of the basal progenitor cells, resulting in a reduction in cortical development. The new mechanism identified deepens our understanding of cerebral cortex development and provides potential therapeutic cues for remedying brain abnormalities stemming from basal progenitor cell deficiency.Abstract Enrichment of basal progenitors (BPs) in the developing neocortex is a central driver of cortical enlargement. The transcription factor Pax6 is known as an essential regulator in generation of BPs. H3 lysine 9 acetylation (H3K9ac) has emerged as a crucial epigenetic mechanism that activates the gene expression program required for BP pool amplification. In this current work, we applied immunohistochemistry, RNA sequencing, chromatin immunoprecipitation and sequencing, and the yeast two-hybrid assay to reveal that the BP-genic effect of H3 acetylation is dependent on Pax6 functionality in the developing mouse cortex. In the presence of Pax6, increased H3 acetylation caused BP pool expansion, leading to enhanced neurogenesis, which evoked expansion and quasi-convolution of the mouse neocortex. Interestingly, H3 acetylation activation exacerbates the BP depletion and corticogenesis reduction effect of Pax6 ablation in cortex-specific Pax6 mutants. Furthermore, we found that H3K9 acetyltransferase KAT2A/GCN5 interacts with Pax6 and potentiates Pax6-dependent transcriptional activity. This explains a genome-wide lack of H3K9ac, especially in the promoter regions of BP-genic genes, in the Pax6 mutant cortex. Together, these findings reveal a mechanistic coupling of H3 acetylation and Pax6 in orchestrating BP production and cortical expansion through the promotion of a BP gene expression program during cortical development.