Figure 2

Mapping functional p53 sites on Alu repeats. The left and right Alu monomers are represented by rectangles; the inter-monomer region and the 3'-tail are shown by lines. Thirteen p53 REs residing in Alu repeats (Table 1) are localized around positions 10, 85 and 150 overlapping with Boxes A, B and A'. The p53 REs are listed according to their localization in Alu, and the ones with spacer S = 0 are underlined. Alignments of selected p53 REs with the corresponding Alu subfamily consensus sequences are shown. The p53 core motifs CNNG and the corresponding regions in Alu elements are highlighted in boldface. The CG dinucleotides are shown in red. Note that the two p53 REs associated with the AIFM2 gene are localized in the same repeat AluJo (Additional File 3: Figure S2) and separated by one superhelical turn of DNA in nucleosome. In such a case, two p53 tetramers can bind cooperatively on the same side of the nucleosomal surface [12], thereby increasing their affinity to DNA. Simultaneous mutations in Boxes A and B (producing two p53 half-sites in the same Alu repeat, separated by S = 75 bp) are likely to happen relatively often. This can explain an unusually frequent occurrence of the spacer S = 75 bp observed earlier [12].