Characterization of Functional Human-Specific Regulatory Elements in Prefrontal Cortical Cells

Understanding the regulatory mechanism of gene expression driven by human-specific cis-regulatory elements (CREs) in adult brain remains elusive. In this study, we investigated the gene regulatory programs in the prefrontal cortex (PFC) of adult human, macaque and mouse using single-nucleus transcriptomic and epigenetic assays from a total of 300,000 cells and characterized human specific gene expression and chromatin accessibility profiles. From these data, we show human-specific candidate CREs (cCREs), including human epigenetic-specific (HES) cCREs and human accelerated regions, play a pivotal role in modulating human-specific gene expression, and human sequencing-specific cCREs are enriched with transposable elements such as ERVK and LINE-1 driving regulatory innovation during human PFC evolution. Integrating with genome-wide association studies, we find high neuropsychiatric relevance of the human-gained chromatin accessibility in PFC. Finally, through machine learning approaches, we nominated a known schizophrenia (SCZ) -associated single-nucleotide polymorphism, rs76095298, which resided in a HES cCRE, as a functional variant that may influence the PITPNM2, a risk gene of SCZ, through creating a binding motif for the transcription factor ETV1, potentially representing a novel therapeutic target for SCZ. In all, our findings provide distinct characteristics of the human-specific epigenetic regulation and simultaneously, a critical insight into evolution and pathological significance of human-specific gene regulation in the adult PFC.