Study / S047EKUTN2024-02-16
Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids
Davide Capauto, Yifan Wang, Feinan Wu, Scott Norton, Jessica Mariani et al.
About this study
Regulation 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 ~7000 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.
Full author list & citation
Davide Capauto, Yifan Wang, Feinan Wu, Scott Norton, Jessica Mariani, Fumitaka Inoue, Gregory E. Crawford, Nadav Ahituv, Alexej Abyzov, Flora M. Vaccarino. Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids. 2024-02-16. https://doi.org/10.1038/s41598-024-54302-7
Experiments 1
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A 270-bp enhancer library was integrated by lentivirus into three independent culture replicates and assayed at the iPSC stage and after terminal differentiation to TD0 and TD30 forebrain organoids. The table retains the authors' QC-passed enhancer and control records and reports MPRAnalyze activity, background p-values, significance calls, linked-gene annotations, predicted TFs, and external ATAC-seq overlaps.