Integrative Omics Reveals Rapidly Evolving Regulatory Sequences Driving Primate Brain Evolution

Although the continual expansion of the brain during primate evolution accounts for our enhanced cognitive capabilities, the drivers of brain evolution have scarcely been explored in these ancestral nodes. Here, we performed large-scale comparative genomic, transcriptomic, and epigenomic analyses to investigate the evolutionary alterations acquired by brain genes and provide comprehensive listings of innovatory genetic elements along the evolutionary path from ancestral primates to human. The regulatory sequences associated with brain-expressed genes experienced rapid change, particularly in the ancestor of the Simiiformes. Extensive comparisons of single-cell and bulk transcriptomic data between primate and nonprimate brains revealed that these regulatory sequences may drive the high expression of certain genes in primate brains. Employing in utero electroporation into mouse embryonic cortex, we show that the primate-specific brain-biased gene BMP7 was recruited, probably in the ancestor of the Simiiformes, to regulate neuronal proliferation in the primate ventricular zone. Our study provides a comprehensive listing of genes and regulatory changes along the brain evolution lineage of ancestral primates leading to human. These data should be invaluable for future functional studies that will deepen our understanding not only of the genetic basis of human brain evolution but also of inherited disease.

Automated summary

By conducting large-scale comparative genomic, transcriptomic, and epigenomic analyses, we investigated the evolutionary changes of brain genes from ancestral primates to humans and provided a comprehensive listing of innovative genetic elements. The regulatory sequences associated with brain-expressed genes underwent rapid changes, particularly in the ancestor of the Simiiformes. Comparisons of primate and non-primate brain transcriptomic data revealed that these regulatory sequences may drive the high expression of certain genes in primate brains. Our study also demonstrated the recruitment of the primate-specific brain-biased gene BMP7 to regulate neuronal proliferation in the primate ventricular zone. These findings provide valuable insights into the genetic basis of human brain evolution and inherited diseases.