TY - JOUR
T1 - Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity
AU - Kosicki, Michael
AU - Laboy Cintrón, Dianne
AU - Keukeleire, Pia
AU - Schubach, Max
AU - Page, Nicholas F.
AU - Georgakopoulos-Soares, Ilias
AU - Akiyama, Jennifer A.
AU - Plajzer-Frick, Ingrid
AU - Novak, Catherine S.
AU - Kato, Momoe
AU - Hunter, Riana D.
AU - von Maydell, Kianna
AU - Barton, Sarah
AU - Godfrey, Patrick
AU - Beckman, Erik
AU - Sanders, Stephan J.
AU - Kircher, Martin
AU - Pennacchio, Len A.
AU - Ahituv, Nadav
N1 - Publisher Copyright:
© The Author(s) 2025.
PY - 2025/12
Y1 - 2025/12
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-025-60064-1
DO - 10.1038/s41467-025-60064-1
M3 - Article
C2 - 40404660
AN - SCOPUS:105005800194
SN - 2041-1723
VL - 16
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 4786
ER -
