Figure 2: Editing in mouse IAP.
From: Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution
(a) An example of DNA editing. The IAP element at chr8:28575443-28581824 (build 37; 6,382 nts) aligns to the element at chr9:114987516-114993954 with 176 G-to-A mismatches and only 26 other mismatches. The G-to-A mismatches are plotted in the top left panel as bars at the coordinates where they occur. The lower left panel shows the much lower number of all other mismatches. The box on the right shows the actual alignment for a segment of 420 nts. The segment contains 32 G-to-A mismatches (red) and only 4 other mismatches (blue). (b) The number of edited IAP elements plotted against the cluster length. The number of elements that contain a C-to-T cluster is plotted as a control. The larger the cluster size we demand, the fewer elements we find, but the higher the confidence that these mismatches occurred because of editing. The threshold P-value for recognizing the cluster as edited was set for convenience as 10−cluster length (Methods). (c) The probabilities of the individual pairs of mismatches across the entire IAP family. The mismatches G⇔A (that is, G-to-A and A-to-G) and C⇔T (C-to-T and T-to-C) are overrepresented, as expected, with a small excess of G⇔A. Mismatches were recorded along all aligned pairs of IAP elements.
