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The genome-wide dual-CRISPR screening identifies essential non-coding regulatory elements

ABSTRACT: Non-coding regulatory elements (NCRE) represent a major fraction of the human genome, play important roles in different biological pathways, and have the potential as genomic medicine targets. We developed a straightforward dual-CRISPR screening system capable of deleting thousands of NCREs genome-wide to study their functions in distinct biological contexts in K562 cells and 293T cells. We show that many NCREs, including ultraconserved elements (UCE), have silencer activity and play essential roles in cell growth and drug response. NCREs with redundant functions could also be identified from the screening data. This dual-CRISPR system is also compatible with single-cell sequencing. We identified that UCE PAX6_Tarzan might be critical in heart development, as removing it from human embryonic stem cells led to defects in cardiomyocyte differentiation. Our study provides further evidence that many NCREs have important biological functions contributing to human biology and diseases, and may serve as future drug targets.

ORGANISM(S): Homo sapiens

PROVIDER: GSE254241 | GEO | 2024/01/28

REPOSITORIES: GEO

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