Extended Data Fig. 6. Impact of GATC-motif mutations on gene expression in MPRA.

(a) Expression change after removing GATC motifs in a pTRP1-based library, plotted as in Fig. 4a. Illustrated effects across 823 fragments (left) and an example fragment with originally 4 motifs (right). (b) Expression changes due to GATC-motifs additions in a pTRP1-based library, mirroring Fig. 4c. Effects across 221 fragments (top) and 4 specific examples (bottom). (c) Pearson’s correlation coefficients between expression of 221 fragments with varying GATC-motif additions in p35S- and pTRP1-based libraries. (d) Influence of GATC-motif additions depends on initial sequence expression. Depicted is the average log₂ expression difference upon motif addition relative to original fragments, for different copy numbers of the added motif. Color indicates original fragment (log₂) expression level ranges, as indicated. Plotted for p35S- (top) and pTRP1-based libraries (bottom). Boxplots in a,b represent the median (center line), IQR (box bounds), whiskers (min and max within 1.5 IQR), and outliers (points beyond whiskers).