Extended Data Fig. 4: PRIME-In mediates efficient targeted integration at therapeutically relevant loci.
a, Editing efficiencies for targeted integration of an EF1α-EGFP reporter with PRIME-In 2.0 across a variety of therapeutically relevant loci, as measured by frequencies of EGFP + HEK293T cell 14 days after transfection. Four to five pairs of sites at each gene locus were evaluated. Three independent biological replicates were performed and the results are shown as the mean ± SD. No statistical comparisons were performed for this screening data. b, Pearson correlation analysis of PRIME-In-mediated integration efficiencies across 48 genomic loci versus PMH GC contents. Integration efficiencies were positively correlated with PMH GC content. c–e, Pearson Correlation analysis of PRIME-In-mediated integration efficiencies across 48 genomic loci and histone marker signals extracted and processed from ChIP-seq data deposited in ENCODE. Integration efficiencies were positively correlated with active histone markers, H3K27ac and H3K4me3, and negatively correlated with heterochromatin marker H3K9me3. Pearson correlation coefficients (r) and P value for each analysis are labelled on the scatter plot. In all cases, P < 0.05 except between PRIME-In and H3K4me3 signal. Integration efficiencies from three individual replicates, measured by frequencies of EGFP+ cells, were averaged and used for analysis. The ChIP-seq signal of each histone modification within a ± 1 kb window centred around the target site was extracted and processed from HEK293T datasets. Statistical significance was calculated using Student’s unpaired two-tailed t-test.
