Fig 1. New approaches for analyzing 3D organization of PCH domains.

(A) Three types of PCH-derived sequences were included in the Hi-C analysis: 1) reads mapped to single-copy sequence in the epigenetically defined PCH regions (“unique” reads, 2.4% of filtered Hi-C reads (see S1 Fig)), 2) reads mapped to known heterochromatic simple and complex repeats (“repeat” reads, 6.44%), or 3) reads mapped to non-unique sequences (dark blue) that are present within epigenetically defined PCH regions (“multi” reads, 3.0%). (B) Methods for assessing if an H3K9me2-enriched euchromatic region displays exceptional 3D contacts with PCH. The observed percentage of euchromatin-PCH read pairs for an H3K9me2 enriched euchromatic region is compared to a null distribution generated using randomly selected, non-H3K9me2 enriched euchromatic regions to estimate p-value.