Species-specific chromatin architecture and neurogenesis mediated by a human enhancer

Genomic modifications underlie the evolution of human features, including a larger neocortex and enhanced cognition. Human Accelerated Regions (HARs) are highly-conserved loci containing human-specific variants and can act as neurodevelopmental enhancers. However, the neurodevelopmental functions of HARs and their mechanism of gene regulation are largely unknown. Here, we show that human ( Hs ) HAR1984 promotes neurogenesis by influencing species-specific transcription and chromatin interactions. Hs-HAR1984 knock-in chimpanzee ( Pt ) cortical organoids contain more progenitors and neurons, whereas Pt - HAR1984 knock-in human cortical organoids exhibit the opposite phenotype. Hs-HAR1984 knock-in mice recapitulate increased neurogenesis, producing a thicker cortex with folding. Hi-C reveals HAR1984 exhibits chromatin looping with its target genes ETV5 and TRA2B in human fetal brains, notably reduced in chimpanzee, macaque and mouse neural cells. We show that human-specific mutations in HAR1984 directly promote these interactions, favored by nearby structural variants. Further, we discover that human-specific ETV5 binding auto-regulates enhancer activity. This work demonstrates new molecular mechanisms underlying human-specific neurodevelopment, linking HARs to chromatin architecture, cortical cell fate and expansion and folding of brains.