Integrative Omics Reveals Rapidly Evolving Regulatory Sequences Driving Primate Brain Evolution

Abstract

Although 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 non-primate 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.

Evolutionary innovation in conserved regulatory elements across the mammalian tree of life

“…Sequence acceleration has previously been found to affect genes with functions related to gene regulation and development in studies investigating single branches in the mammalian tree of life [Pollard et al 2006, Holloway et al 2016, Bi et al 2023, Zhuang et al 2023]. When we inspected acceleration on a single branch, this pattern was not always apparent, but it was prominent in our analysis across the entire mammalian tree.…”

Decoding DNA sequence-driven evolution of the human brain epigenome at cellular resolution

“…Functional mechanisms of these elements are investigated both per candidate region 7,8 and across all candidate regions using functional omics strategies [9][10][11] . More recent studies have also focused on evolutionary changes in the ancestral lineages of humans that offer additional insight into the composition of the human genome 12,13 .…”