Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids

AO_SCPLOWBSTRACTC_SCPLOWRegulation of gene expression through enhancers is one of the major processes shaping the structure and function of the human brain during development. High-throughput assays have predicted thousands of enhancers involved in neurodevelopment, and confirming their activity through orthogonal functional assays is crucial. Here, we utilized Massively Parallel Reporter Assays (MPRAs) in stem cells and forebrain organoids to evaluate the activity of [~]7,000 gene-linked enhancers previously identified in human fetal tissues and brain organoids. We used a Gaussian mixture model to evaluate the contribution of background noise in the measured activity signal to confirm the activity of [~]35% of the tested enhancers, with most showing temporal-specific activity, suggesting their evolving role in neurodevelopment. The temporal specificity was further supported by the correlation of activity with gene expression. Our findings provide a valuable gene regulatory resource to the scientific community. AO_SCPLOWUTHORC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSUMMARYC_SCPLOWEnhancers are non-coding elements that play a crucial role in the regulation of gene expression during brain development. Despite the availability of various techniques available to identify enhancers, their functional activity is relatively less understood, leaving a gap in our understanding of how enhancer behavior might regulate complex transitions of neurodevelopment. To address this, we utilized forebrain organoids, a 3D model system which closely mimics the complex cellular environment of the developing human brain, and employed Massively Parallel Reporter Assay (MPRA) to validate enhancer activity at various stages of forebrain differentiation, from induced pluripotent stem cells (iPSCs) to neuronal progenitors and cortical neurons. Our study provides a comprehensive catalog of over 2,300 enhancers, showcasing their temporal activity profiles during early neuronal development and offering valuable insights into their likely biological functions. This research advances our understanding of enhancer dynamics in brain development and offers new avenues for further investigations in this field.