PAGE 11 OF 15 Nucleic Acids Research, 2007, Vol. 35, No. 16 e106 Figure 7. Polygon ﬁber of 65 nucleosomes (a = 908) with a random b sequence (shown in Figure 8). (A) Relaxed ﬁber. (B) Stretched ﬁber. (C) Loop formation by interaction of nucleosome No. 1–5 with nucleosome No. 65. Stable loop clustering is indicated by brackets. (D–F) Nucleosome interactions in (A, B, C). Clusters of stable and ﬂexible loops are shown in red and blue regions, respectively, and nucleosomes with relative stable and variable mutual positions are black and gray, respectively. (G–I) Compaction of nucleosome No. 1–20 (G), 1–40 (H) and 1–65 (I) after chromatin remodeling and twisting of the linkers to form b sequence (333)n, as shown in Figure 8. Bar = 30 nm. varying up to b( 3) around a mean value of b(0). Such ﬁbers could not be folded with high precision, and were therefore made in triplicate in order to account for minor inaccuracies, which will inevitably aﬀect the mutual orientation of nearby nucleosomes. Figure 7 shows a model of a polygon ﬁber consisting of 65 nucleosomes (a = 908) with the b sequence shown in Figure 8. Analysis of three models of this ﬁber showed the presence of clustered loops of 4–13 nucleosomes (Table 1). One class consisted of loops formed by nucleosomes, which tended to stay in touch in all three models (black in Figure 7D-F). In the model in Figure 7, these nucleosomes were even not separated by a mild stretch of the ﬁber, thus forming relatively stable domains. A second class consisted of loops formed by nucleosomes, which were more unstably associated (gray in Figure 7D-F), being separated by even a mild stretch of the ﬁber and showing a more variable mutual localization in the three models. Both types of clusters were connected by more ﬂexible segments of the ﬁlament with nucleosomes, which were generally not in touch with other nucleosomes (white in Figure 7D-F). Because of a high ﬂexibility mainly in these regions, the ﬁber easily formed loops by contacts between nucleosomes at the ends of the ﬁber. The loop shown in Figure 7C was stabilized by nucleosome No. 65 ﬁtting into a pocket Figure 8. b sequences of the polygon ﬁber shown in Figure 7. The original sequence was remodeled by moving nucleosomes the number of base pairs indicated in the directions shown by the arrows. The resulting b sequence is shown in the second row, the changed b values being indicated by a gray background. The third row shows the b sequence (333)n after twisting of the linkers within the twist constraints.