Figure 6. Nup93 contributes to long-range interactions between distant Polycomb sites.

(A) Average genome-wide Hi-C interactions between Pc domains that contain Nup93 ChIP-seq peaks (Nup93+), Pc domains that do not (Nup93-) and regions that do not contain Pc (Neither). Average Hi-C interactions between the whole genome and these categories are plotted for comparison (right). Hi-C signal obtained from existing Hi-C datasets (described in text). Note preferential interactions of Nup93+/Pc regions with each other. P-values calculated using two-tailed nonparametric t test. (B) Violin plot of distributions of measured distances between centers of Fab-7 and ss probes in Kc cells, treated with RNAi as indicated. Horizontal lines depict median (dashed) and quartiles. > 200 cells per condition, 2–4 biological replicates. P values are from a two-tailed unpaired non-parametric t test. (C) Fraction of cell population with Fab-7-ss probe interaction distance greater than 1um, in cells treated as described in (B). (D) Representative images of cells treated as described in (B). Cells are co-labeled with Oligopaint FISH probes for Fab-7 (red) and ss (cyan), IF against Lamin (green), and stained DNA (DAPI, blue). Scale bar 5um. (E) 3C crosslinking frequencies between Fab7 and genomic regions along the Abd-B locus in S2 cells, treated as described. The relative interaction frequencies are plotted against genomic coordinates and aligned with chromatin binding maps of Nup93 and Pc. Black tick marks indicate Hind III restriction sites, vertical dotted lines correspond to the fragments investigated, hollow triangles indicate the primers tested. The primer of the anchor point is represented by a black triangle and the grey bar marks the position of the fixed Hind III fragment. Bars represent mean + SEM from 6 independent experiments. P values are from a two-sided t test. See also Figure S6.