An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

ABSTRACT: We developed a new framework for highly powered, unbiased CRISPR screens of distal regulatory elements, including an optimized experimental method (Direct-Capture Targeted Perturb-seq (DC-TAP-seq)), a random design strategy, and a comprehensive analytical pipeline that accounts for statistical power. Using pilot datasets from K562 and WTC11 cells, we benchmarked DC-TAP-seq against conventional scRNA-seq and TAP-seq for capture efficiency, guide detection, and knockdown assessment. Applying this optimized framework, we systematically perturbed ~1,400 randomly selected candidate regulatory elements across the two cell types and revealed key features of the human regulatory landscape. We found that most regulatory interactions have small effect sizes (<10%), occur over short genomic distances (<100 kb), and often involve CTCF-bound elements lacking classical enhancer marks. Housekeeping genes were regulated by distal elements with ~2-fold weaker effect sizes compared to other genes. Our results highlight limitations in existing CRISPR datasets and predictive models, and demonstrate the utility of DC-TAP-seq for building more comprehensive maps of distal regulation in the human genome.

ORGANISM(S): Homo sapiens

PROVIDER: GSE303901 | GEO | 2025/08/15

REPOSITORIES: GEO