CRISPR-CLEAR: Nucleotide-Resolution Mapping of Regulatory Elements via Allelic Readout of Tiled Base Editing

CRISPR tiling screens have advanced the identification and characterization of regulatory sequences but are limited by low resolution arising from the indirect readout of editing via guide RNA sequencing. This study introduces CRISPR-CLEAR, an end-to-end experimental assay and computational pipeline, which leverages targeted sequencing of CRISPR-introduced alleles at the endogenous target locus following dense base-editing mutagenesis. This approach enables the dissection of regulatory elements at nucleotide resolution, facilitating a direct assessment of genotype-phenotype effects. Overall design: Tiling mutagenesis of the CD19 enhancer in ABE8e-SpRY and evoCDA expressing NALM-6 cell lines. Cells were stained with a fluorescently conjugated antibody used to assess expression of CD19. After staining, cells were sorted using fluorescence-activated cell sorting into a "CD19 positive" and "CD19 negative" population. Genomic DNA was extracted from these populations and split into half – half was used for the traditional guide RNA sequencing approach and in the other half the endogenously targeted region was directly sequenced. A follow-up experiment involving a single guide, sg218, was also performed.