Fig. 2
From: High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases
Determinants of Cre:loxP specificity identified by Rec-seq on wild-type Cre and Ala-substituted Cre variants. a Protein:DNA contacts for Cre:loxP inferred from crystal structures8. b Rec-seq enrichment profile for the CreR259A variant (red line) and wild-type Cre (gray line). c Heat map of Rec-seq enrichment values for the CreR259A variant showing the log2 of the enrichment value for each nucleotide at each position in loxP relative to the canonical base (black outline). d–f Rec-seq enrichment profiles for Ala-substituted Cre mutants (colored lines) and wild-type Cre (gray lines). For b–f values represent the geometric mean of n = 3 or n = 11 (wild-type Cre) independent replicates (dots) conducted at 37 °C for 30 min at a 1:3 protein:DNA ratio. g The results of Rec-seq experiments on wild-type Cre (black dots) and variants thereof (colored dots) visualized using t-SNE multi-dimensional proximity analysis37, showing that experimental replicates are clustered by similarity across all specificity features. Significant differences (p ≤ 0.05) relative to wild-type Cre at individual nucleotides (Student's t-test; colored asterisks) and across the full log-enrichment profile (Mann-Whitney U test; ‡) are indicated. Source data are provided as a Source Data file
