RT Journal
A1 Gaynor-Gillett, Sophia C.
A1 Cheng, Lijun
A1 Shi, Manman
A1 Liu, Jason
A1 Wang, Gaoyuan
A1 Spector, Megan
A1 Guo, Qiuyu
A1 Qi, Le
A1 Flaherty, Mary
A1 Wall, Martha
A1 Hwang, Ahyeon
A1 Gu, Mengting
A1 Chen, Zhanlin
A1 Chen, Yuhang
A1 PsychENCODE Consortium
A1 Moran, Jennifer R.
A1 Zhang, Jing
A1 Lee, Donghoon
A1 Gerstein, Mark
A1 Geschwind, Daniel
A1 White, Kevin P.
T1 A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
JF Genome Research 
JO Genome Research 
YR 2025 
FD August 01 
VO 35 
IS 8 
SP 1887 
OP 1901 
DO 10.1101/gr.279584.124 
UL http://genome.cshlp.org/content/35/8/1887.abstract 
AB Genome-wide association studies (GWASs) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. Here, we perform capture STARR-sequencing of over 70,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We select candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWASs. Over 8000 regions demonstrate enhancer activity in the phNPCs, and we link these regions to over 2200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including neuronal system, nervous system development, and developmental delay. We functionally validate a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identify thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.