A human-specific enhancer fine-tunes radial glia potency and corticogenesis

Abstract

Humans evolved an extraordinarily expanded and complex cerebral cortex, associated with developmental and gene regulatory modifications ^1-3 . Human accelerated regions (HARs) are highly conserved genomic sequences with human-specific nucleotide substitutions. Although there are thousands of annotated HARs, their functional contribution to human-specific cortical development is largely unknown ^4,5 . <i>HARE5</i> is a HAR transcriptional enhancer of the WNT signaling receptor <i>Frizzled8 (FZD8)</i> active during brain development ⁶ . Here, using genome-edited mouse and primate models, we demonstrate that human <i>(Hs) HARE5</i> fine-tunes cortical development and connectivity by controlling the proliferative and neurogenic capacity of neural progenitor cells (NPCs). <i>Hs-HARE5</i> knock-in mice have significantly enlarged neocortices containing more neurons. By measuring neural dynamics <i>in vivo</i> we show these anatomical features correlate with increased functional independence between cortical regions. To understand the underlying developmental mechanisms, we assess progenitor fate using live imaging, lineage analysis, and single-cell RNA sequencing. This reveals <i>Hs-HARE5</i> modifies radial glial progenitor behavior, with increased self-renewal at early developmental stages followed by expanded neurogenic potential. We use genome-edited human and chimpanzee (Pt) NPCs and cortical organoids to assess the relative enhancer activity and function of <i>Hs-HARE5</i> and <i>Pt-HARE5.</i> Using these orthogonal strategies we show four human-specific variants in <i>HARE5</i> drive increased enhancer activity which promotes progenitor proliferation. These findings illustrate how small changes in regulatory DNA can directly impact critical signaling pathways and brain development. Our study uncovers new functions for HARs as key regulatory elements crucial for the expansion and complexity of the human cerebral cortex.