Polycomb Domains Interact in Nuclear Space Figure 6. Long-range interactions predominantly occur within a single chromosome arm. (A) Domainograms show two illustrative examples of genome-wide interaction maps using either Abd-B (top) or trh (bottom) as bait. Plots are described in Figure 1B and Figure 2. Note, the small repeat-rich chromosome 4 is not shown. (B) Bar plots depict fraction of interactions within bait containing chromosome arm (black) and interactions with other chromosome arms (white). Bait names are indicated (x-axis) as well as absolute number of interactions (top). Across eight data sets we identified 201 interactions (all), of which ,95% are limited to a single chromosome arm, which also contains the bait sequence, and only 5% occurs between sequences on two chromosome arms. doi:10.1371/journal.pgen.1001343.g006 detect significant changes relative to wild type gene expression, when we compared genes residing on either 3LIN, 3RIN, or other chromosome arms (Figure S4). We additionally performed genetic experiments to test whether gene expression is altered on the In(3LR)sep chromosome. Sex combs reduced (Scr) expression levels in larval imaginal discs correlate strongly with the number of sex comb teeth on adult male 1st thoracic legs [30,31]. We further sensitized Scr expression by crossing either the wild type or In(3LR)sep chromosome to several Scr-mutant alleles. As expected, we observed approximately 6 to 7 sex comb teeth per leg on average for the Scr/3RWT (functional Scr allele on wild type chromosome 3R) heterozygous animals (Figure S4) [31]. We observed similar numbers on Scr/3LIN flies, which carry the functional Scr allele on inverted chromosome (Figure S4). Taken together, our experiments failed to detect altered gene expression on the In(3LR)sep chromosome. We further examined the interactions on the In(3LR)sep chromosome, and observed that, like on the wild type chromo- some, Abd-B and Antp prefer to contact other PcDs. We observed PcD-specific interactions for 4 out of 6 new Abd-B contacts on the 17 Mbp that rearranged from 3LWT to 3RIN (Figure 7B, left). In addition, Antp showed 7 PcD-specific interactions out of 10 new PLoS Genetics | www.plosgenetics.org 8 March 2011 | Volume 7 | Issue 3 | e1001343