Figure 1. Long-range chromatin contacts of the Pou5f1 bait region in ESCs.

A, Pooled 4C-seq data set, depicting the interaction profile of the Pou5f1 locus located on chromosome (chr) 17 in mouse ESCs. (i) Average hit probability (Hit%) within 200kb windows tiled across the genome. (ii) Hit% in cis (thresholded as displayed) was compared to an empirically modeled background hit% (iii) using the binomial test. (iv) Binomial test results and (v) significantly interacting domains of the Pou5f1 bait region (based on −log(p-values)>=1.8). The vertical red line and associated gray bar denote the Pou5f1 bait locus and the extended 1Mb bait region, respectively, which is always excluded from downstream analysis of the Pou5f1 interactome.

B, Significantly interacting domains (blue) of the Pou5f1 bait region (red), genome-wide.

C, DNA FISH-based 3D distance measurements between the Pou5f1 locus and genomic regions marked by A-C (in cis) or by D (in trans). Based on 4C-seq data, A and B interact with the Pou5f1 locus, but C, located in an intervening genomic region closer to Pou5f1 on linear DNA than B, does not. Boxes demarcate the interquartile range (IQR) and median, and whiskers +/−1.5 times the IQR. *=p-value<0.05, ***=p-value<0.001, Wilcoxon rank-sum test.

D, Two genomic regions containing the gene Prss22 and 1700067P10Rik were identified as interacting partners of the Pou5f1 locus. 4C-seq experiments using Prss22 and 1700067P10Rik as bait regions confirmed their interaction with Pou5f1. Bait regions, 4C-seq hit%, and interacting domains are shown.

See also Figure S1.