Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

Correlation with predicted G4 motifs and CpG islands. (A) The −log₁₀ (P-value) signal for LexoG0_G0gDNA, NS_G0gDNA, and NS_LexoG0 for a 48-kb region on the q arm of Chromosome 19 containing a repeated array of CpG islands. (B,C) Density of G4 motifs and LexoG0_G0gDNA, NS_G0gDNA, and NS_LexoG0 peaks on Chromosome 3 (B) and Chromosome 6 (C). (D) Scatterplot of genome-wide densities (counts in 100-kb bins) of LexoG0_G0gDNA, NS_G0gDNA, and NS_LexoG0 peaks and predicted G4 motifs. Pearson's r and Spearman's ρ for the densities of the indicated sample and G4 motifs are displayed in the box, along with the percentage of overlap of peaks with predicted G4 motifs (peaks vs. G4) or vice versa (G4 vs. peaks) for each data set. For all panels, cyan, LexoG0_G0gDNA; blue, NS_G0gDNA; and green, NS_LexoG0.