Polycomb Domains Interact in Nuclear Space Figure 7. Interactions are constrained by chromosome architecture. (A) A schematic overview of the wild type and inverted chromosome 3. The wild type strain used in this study (w1118) is shown on top. Dashed lines indicate the annotated positions of the break points (BK1 and BK2) present in the inverted chromosome of In(3LR)sep (bottom). Sequences on the inverted left arm 3LIN are red and 3RIN blue. Positions of the baits are indicated. (B–C) Domainograms show interactions of Abd-B (B) and Antp (C) on the inverted third chromosome. Note that all domainograms are plotted in the wild type orientation, which allows direct comparison with wild type data (Figure 2B, 2C). The colors on the x-axes indicate location on inverted chromosome (red = 3LIN; blue = 3RIN). Exact positions of the break points are highlighted by dashed vertical lines. Rest of plot details are described in Figure 1B and Figure 2. doi:10.1371/journal.pgen.1001343.g007 contacts with sequences that originate from 3LWT and are now on 3LIN (Figure 7C, left). All together, a highly significant fraction (70% for Antp and 74% for Abd-B) of all DIDs coincide with PcDs (Figure 8B) and K27Ds (data not shown). In summary, we conclude that on the In(3LR)sep chromosome Abd-B and Antp preferentially contact PcDs that are located on the same chromosome arm, demonstrating that interactions are constrained by the overall chromosome architecture. Figure 8. On the inverted third chromosome Homeotic genes preferentially contact PcDs located on the same chromosome arm. (A) Bar plots show quantification of interactions within single chromosome arm and between two chromosome arms in brain tissue from In(3LR)sep larvae. Plot is described in Figure 6B. Like on the wild type third chromosome (Figure 6B), on the inverted third chromosome 95% of all interactions are intrachromosomal and only 5% is interchromosomal. (B) Proportion of DIDs that overlap with PcDs. Plot is described in Figure 3A. doi:10.1371/journal.pgen.1001343.g008 PLoS Genetics | www.plosgenetics.org 9 March 2011 | Volume 7 | Issue 3 | e1001343