Figure 4

Variability in DNA structural characteristics between insertion sites for various vectors. All (a) A-philicity, (b) trinucleotide bendability, and (c) V _step values were summed across 12 nucleotides and averaged for all sites of each vector class. (d) 'Jaggedness' was measured by taking the absolute value of differences between adjacent V _step values, which were then summed and averaged, as in panels a to c. Error bars represent standard deviations. 'SB' indicates 574 Sleeping Beauty integrations into human cells identified by Yant and coworkers [106]. 'SB preferred' indicates a subset of 189 sites from the Yant dataset classified as 'preferred' by ProTIS [116]. 'tol2' indicates 63 Tol2 integrations [89]. 'piggyBac' indicates 297 piggyBac insertions deposited into Genbank by Exelexis containing a single TTAA sequence flanked by 10 bases on each side. 'P-element' indicates 920 P-element insertion sites mapped by Liao and coworkers [130]. 'ASV' indicates 357 avian sarcoma leukosis virus (ASLV) insertions into 293T-TVA cells. 'HIV' indicates 334 HIV integrations into SubT1 cells. 'MLV' indicates 695 murine leukemia virus integrations into HeLa cells. 'SIV' indicates 148 simian immunodeficiency virus integrations into CEMx164 cells. All P-element, ASV, HIV, MLV, and SIV sequences were kindly provided by Dr Xioalin Wu. All sites were compared with three sets of over 9,000 randomly selected 12-mers from 10 megabase sections of human chromosome 1 (Hs), mouse chromosome 4 (Mm), and Drosophila chromosome 3L (Dm), and 10,000 randomly selected TA and TTAA sites from human chromosome 1.