CRISPR-based functional screening of noncoding regulatory elements

The vast majority of trait-associated genetic variants reside in noncoding cis-regulatory elements (CREs), yet most regulatory sequences remain functionally uncharacterized. CRISPR-based screens enable direct perturbation of CREs in their native genomic context and have expanded into a diverse toolkit, including CRISPRi/CRISPRa, nuclease-mediated editing, base editing, prime editing, and continuous mutagenesis. Moreover, these approaches can be paired with phenotypic, transcriptomic, or chromatin readouts at single-cell resolution. However, a limitation of conventional pooled CRISPR screens is that cells are assigned by sgRNA identity rather than by the genotype installed. New genotype-resolved approaches address this gap by directly reading the edited endogenous sequence. Because sequence variants in CREs are associated with human disease, continued development of CRISPR-based technologies may help advance new therapies. In this review, we discuss diverse CRISPR-based modalities and their limitations, emerging genotype-resolved techniques, their applications in gene therapy, and computational approaches for predicting the function of regulatory sequences.

Abstract from PubMed (PMID 42933312). This entry was added automatically by our daily literature monitor because it matches the topics we follow; read the full paper at the original source.