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Abstract
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.
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Details
1 Yale University, Child Study Center, New Haven, USA (GRID:grid.47100.32) (ISNI:0000 0004 1936 8710)
2 Mayo Clinic, Department of Quantitative Health Sciences, Center for Individualized Medicine, Rochester, USA (GRID:grid.66875.3a) (ISNI:0000 0004 0459 167X)
3 Kyoto University, Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan (GRID:grid.258799.8) (ISNI:0000 0004 0372 2033)
4 Duke University, Department of Pediatrics, Durham, USA (GRID:grid.26009.3d) (ISNI:0000 0004 1936 7961)
5 University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811); University of California, San Francisco, Institute for Human Genetics, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)
6 Yale University, Child Study Center, New Haven, USA (GRID:grid.47100.32) (ISNI:0000 0004 1936 8710); Yale University, Department of Neuroscience, New Haven, USA (GRID:grid.47100.32) (ISNI:0000 0004 1936 8710); Yale University, Yale Stem Cell Center, New Haven, USA (GRID:grid.47100.32) (ISNI:0000 0004 1936 8710)