Figure 3

Distribution of the nucleotide substitutions in the IAPE-D and HERV-K genomic copies residing in the mouse and human genomes. Endogenous sequences were extracted from the mouse and the human genome databases, aligned and compared to the derived consensus. (A) Upper panels: percentage of substitutions for each nucleotide, for the endogenous IAPE-D and HERV-K elements (with the IAPE-A elements used as a control). Lower panels: two-entry tables showing nucleotide substitutions preferences, with the G-to-A values in bold (higher that the "non-specific" C-to-T value for IAPE-D and HERV-K, and identical in the case of the IAPE-A control). n, total number of nucleotides analyzed. (B) Influence of nucleotides at position -2, -1, +1 and +2 on G-to-A mutations (the mutated G is at position 0). Data represent the percentage of indicated target di- or trinucleotide sequences bearing G-to-A mutations. X represents any nucleotide. P-values calculated for the two-entry tables (in A) by a Poisson regression in a log-linear model for the occurrence of the G-to-A versus C-to-T mutations yielded p < 0.003 for IAPE-D and HERV-K; in B, p-values calculated by a chi square test were p < 0.001; similar levels of significance were obtained using the Kruskal Wallis test. (C) Example of G-to-A mutations present in twenty IAPE-D (upper panel) and HERV-K (lower panel) sequences. GXA trinucleotides and GG dinucleotides are underlined in the consensus sequence of IAPE-D and HERV-K, respectively.