Chengyu Deng, Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F. Przytycki et al.
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type–specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.
Chengyu Deng, Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F. Przytycki, Fumitaka Inoue, Daniela A. Pereira, Davide Capauto, Scott Norton, Flora M. Vaccarino, Alex A. Pollen, Tomasz J. Nowakowski, Nadav Ahituv, Katherine S. Pollard, PsychENCODE Consortium. Massively parallel characterization of regulatory elements in the developing human cortex. 2024-05-24. https://doi.org/10.1126/science.adh0559
The 270-bp brain QTL and psychiatric-disorder-associated variant library was tested with reference and alternative alleles in approximately 10-week human cortical organoid slices. The table retains allele-specific RNA/DNA activity, limma statistics, and the supplied regulatory annotations.
A 270-bp variant library centered on brain QTLs and psychiatric-disorder-associated variants was tested in GW18 primary human cortical cells with reference and alternative alleles. Allelic enhancer activity is represented by the alternative/reference RNA/DNA ratio and limma differential-activity statistics.
The 270-bp differentially accessible candidate regulatory-element library was tested with lentiMPRA in approximately 10-week human cerebral organoid cortical slices. Barcode RNA/DNA ratios quantify enhancer activity, with the supplied cell-type accessibility, DA, chromatin-loop, ABC, motif, and conservation annotations retained.
A 270-bp differentially accessible (DA) candidate regulatory-element library was tested with lentiMPRA in GW18 primary human cortical cells. Barcode RNA/DNA ratios quantify enhancer activity, with cell-type accessibility, DA, chromatin-loop, ABC, motif, and conservation annotations retained.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
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