Kosicki Michael, Laboy Cintrón Dianne, Keukeleire Pia, Schubach Max, Page Nicholas F, Georgakopoulos-Soares Ilias, Akiyama Jennifer A, Plajzer-Frick Ingrid, Novak Catherine S, Kato Momoe, Hunter Riana D, von Maydell Kianna, Barton Sarah, Godfrey Patrick, Beckman Erik, Sanders Stephan J, Kircher Martin, Pennacchio Len A, Ahituv Nadav
Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA.
Nat Commun. 2025 May 23;16(1):4786. doi: 10.1038/s41467-025-60064-1.
High-throughput massively parallel reporter assays (MPRAs) and phenotype-rich in vivo transgenic mouse assays are two potentially complementary ways to study the impact of noncoding variants associated with psychiatric diseases. Here, we investigate the utility of combining these assays. Specifically, we carry out an MPRA in induced human neurons on over 50,000 sequences derived from fetal neuronal ATAC-seq datasets and enhancers validated in mouse assays. We also test the impact of over 20,000 variants, including synthetic mutations and 167 common variants associated with psychiatric disorders. We find a strong and specific correlation between MPRA and mouse neuronal enhancer activity. Four out of five tested variants with significant MPRA effects affected neuronal enhancer activity in mouse embryos. Mouse assays also reveal pleiotropic variant effects that could not be observed in MPRA. Our work provides a catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays.
高通量大规模平行报告基因检测（MPRAs）和富含表型的体内转基因小鼠检测是研究与精神疾病相关的非编码变异影响的两种潜在互补方法。在此，我们研究了结合这些检测方法的实用性。具体而言，我们在诱导的人类神经元中对来自胎儿神经元ATAC-seq数据集和在小鼠检测中验证的增强子的50000多个序列进行了MPRA。我们还测试了20000多个变异的影响，包括合成突变和167个与精神疾病相关的常见变异。我们发现MPRA与小鼠神经元增强子活性之间存在强烈且特定的相关性。在具有显著MPRA效应的五个测试变异中，有四个影响了小鼠胚胎中的神经元增强子活性。小鼠检测还揭示了在MPRA中无法观察到的多效性变异效应。我们的工作提供了功能性神经元增强子和变异效应的目录，并突出了结合MPRAs和小鼠转基因检测的有效性。
