De novo human brain enhancers created by single nucleotide mutations

Advanced human cognition is attributed to an evolutionary increase in size and complexity of the neocortex. However, the underlying gene regulatory mechanisms are poorly understood. Here, based on a deep learning model of embryonic neocortical enhancers capable of assessing functional effects of mutations, and human and macaque embryonic neocortex H3K27ac data, we identified ~4000 enhancers gained in the human lineage, largely attributable to single-nucleotide essential mutations. The genes near these gained enhancers exhibit an increased expression in human embryonic neocortex and are involved in critical neural developmental processes, and are expressed specifically in the progenitor cells and interneurons that connect different brain regions and are involved in cell/axon migration. As a consequence, gained enhancers are strongly associated with central nervous system disorders. We show that the essential mutations have evolved under relaxed purifying selection and affect binding of key transcription factors. We identified a putative core transcriptional network induced by the gained enhancers, with POU3F2 occupying a central position. Our results suggest that non-coding mutations have led to de novo enhancer gain in the embryonic human neocortex, establishing a core network that regulates the expression of genes involved in critical developmental processes and potentially orchestrating the evolution of human cognition.