Polycomb Domains Interact in Nuclear Space Figure 4. Non-target genes interact with other sequences than PcG target genes. (A) Position of four 4C baits that are not PcG target genes (red), plotted as in Figure 2A. (B–E) Long-range chromatin interactions for Wnt inhibitor of Dorsal (wntD - B), CG5107 (C), Calreticulin (Crc - D), and RNA polymerase II 140 kD subunit (RpII140 - E). Plots are as in Figure 1B and Figure 2. doi:10.1371/journal.pgen.1001343.g004 Long-range interactions are predominantly limited to a single chromosome arm We noticed that long-range interactions of all our baits predominantly occur within the same adult chromosome arm (Table S2). For example, Abd-B only interacts with sequences on chromosome 3R (Figure 6A). However, we also identified rare cases of interactions between loci on different chromosome arms. For instance, the Ptx1 locus (chromosome 3R) interacts with a discrete region on the X, and Antp with a PcD on chromosome 4 (Table S2). The highly expressed Crc (chromosome 3R) gene interacts with two regions on chromosome 3L and one on chromosome 4, indicating that not only PcG targets can interact with other chromosome arms. Finally, the trh gene (chromosome 3L) shows the highest frequency of interactions with other chromosome arms (Figure 6A), although this only represents 19% of all DIDs (i.e. 6 out of 31). We observed that between 81 and 100% of all interactions for all eight bait sequences occur within a single chromosome arm (Figure 6B). When we combined all data, we observed that on average 95% of all interactions (n = 201) are limited to a single PLoS Genetics | www.plosgenetics.org 6 March 2011 | Volume 7 | Issue 3 | e1001343