Figure 3

Approaches to identification of DNA structural characteristics governing insertion site preferences for Tol2 and SB transposons. (a) Averaging of all available insertion sites smoothes trends observed in individual plots. Plot of V _step profiles of 18 20-base-pair Tol2 insertions (left, from Balciunas and coworkers [89]) compared with 18 randomly generated sequences (right). Averages are shown by thick black lines. Although individual Tol2 profiles appear jagged, peaks are not position specific, and so the plot of the average of 36 sites reveals only one small, distinct peak. Individual random sequences also appear jagged, but an average of over 9,000 random sequences is a flat line. (b) Analyses of Tol2 insertion site A-philicity profiles, compared with 18 random sequences. Trends are similar to V _step patterns. (c) Plot of trinucleotide bendability for Tol2 and random sites, indicating only small common trends compared with random sequence. The random sequences in panels a to c were acquired from a 10 megabase portion of human chromosome 1p. (d) Bendability plots for Sleeping Beauty (SB) insertion sites (from Yant and coworkers [106]). The average trinucleotide bendability at each position of 12-base insertion sites is shown for 574 insertions ('all sites'), as well as a subset of 189 insertions classified as 'preferred' based on V _step profiles ('preferred sites'). Random TA sites are shown in green, and random sites in black. This plot shows how identification of 'preferred' sites can be useful in distinguishing structural patterns for common insertion sites; preferred sites (based on common patterns of protein-induced deformability in recurrently hit sites) exhibit an overall increase in a separate parameter, DNA bendability, when 'basal' sites are removed.