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Figure 7 | Biology Direct

Figure 7

From: Impact of Alu repeats on the evolution of human p53 binding sites

Figure 7

Experimentally mapped nucleosomes and predicted p53 BSs in Alu elements. (A) The two mapped nucleosomes (magenta ellipses) are shown together with the three clusters of p53 sites near positions 10 (Box A), 85 (Box B) and 150 (Box A'). For each cluster, the prevalent spacer S is indicated (Figures 2 and 4). The fragment of Alu consensus sequence is presented (positions 120 to 170), with the 20 bp-long counterpart of the predicted p53 site colored in red and blue. The underlined dimers correspond to the base pairs shown as the red and blue balls in the left part of Figure 7B. The approximate in vitro nucleosome position in the right Alu monomer has been established by Englander and Howard [37]. The shown dyad position 207 corresponds to the optimal rotational setting of this nucleosome - see main text. (B) Exposure of the p53 site embedded in the nucleosome mapped on the right Alu monomer (covering the interval from 134 to 280). Right: The histone octamer is shown as a cylinder and DNA is represented by ribbons (sugar-phosphate backbone) and balls (centers of base pairs). The blue balls indicate the dimeric steps where DNA is bent into the minor groove [79]. For the 'posterior' half of nucleosome, the DNA axis is represented by grey sticks. Left: The p53-DNA complex (Figure 1) is shown schematically with four ellipses representing the p53 tetramer bound to a 20-bp DNA fragment (spacer S = 0). The DNA axis is represented by sticks and balls. The red balls stand for the centers of the CNNG core motifs bent into the major groove, and the blue ones for the junction between two half-sites bent into the minor groove (underlined in Figure 7A). Note that conformation of the DNA fragment bound by p53 tetramer (on the left) closely resembles conformation of the 20 bp-long fragment of nucleosomal DNA centered at position 150 (on the right). Therefore, the p53 site embedded in nucleosome at this position is likely to be accessible for p53 binding. Centers of the other accessible sites are shown by blue balls.

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