HIV favors integration in the major grooves of DNA on nucleosomes. Positions of HIV integration sites on nucleosomes were predicted based on the chicken nucleosome prediction model developed by Segal et al. (2006). The percentage of integration events occurring on nucleosomes is shown for each DNA position relative to the symmetric dyad axis (position 0): (A) 19,962 HIV-Avr sites (gray) and 59,763 matched random control sites for Avr (black line); (B) 20,607 HIV-Mse sites (gray) and 61,692 matched random control sites for Mse (black line). (C, D) Fourier transformation of the data from A and B, respectively, showing periodicity for both HIV-Avr and HIV-Mse.