Characterization of functional human-specific regulatory elements in prefrontal cortical cells

Understanding how human-specific cis-regulatory elements (CREs) drive gene expression in the adult brain remains elusive. Here, we profile the prefrontal cortex (PFC) of adult human, macaque, and mouse using single-nucleus transcriptomic (106,266 cells) and genome-wide chromatin accessibility (212,099 cells) assays, showing human-specific gene expression and chromatin accessibility. We find that human-specific candidate CREs (cCREs) are central in modulating human-biased expression, and those unique to the human genome are enriched with transposable elements such as endogenous retrovirus-K (ERVK) and long interspersed nuclear element 1 (LINE-1), suggesting a role in regulatory innovation during PFC evolution. Genome-wide association analyses indicate strong neuropsychiatric relevance of human-gained accessibility, and machine learning prioritizes disorder-associated single-nucleotide polymorphisms within these cCREs as potential functional variants influencing disease-risk genes, likely via altered transcription factor binding. In all, our findings provide distinct characteristics of human-specific transcriptional regulation and, simultaneously, a critical insight into evolution and pathological significance of human-specific gene regulation in the adult PFC.