Fig. 4

Hi-C analysis of WT-v-Peril KO mESC. a Chromatin contact map surrounding the Peril locus at 20-kb resolution using custom mm10 genome build in wild-type (top) and knockout (bottom). Genes indicated below, with genes of interest indicated in red. TAD borders indicated in black; − 1 and + 1 TADs demarcated by gray box while Peril-containing TAD is demarcated by a black box. b Mapping strategy of the Hi-C data to a custom mm10 mouse genome, where the deleted Peril region (~ 14.5 kb) is replaced by Ns and this sequence or the LacZ (~ 3.5 kb) are compiled as separate chromosomes. 3′ shoulder region (not affected by deletion, but used as a bait region common to both WT and KO conditions) indicated in red. c Digital 4C summary of normalized interactions between the 3′ shoulder region (chr3:34784809–34800385) and the + 1 TAD in either WT or KO. d Digital 4C plots of the interaction anchored on either Mccc1 or Exosc9 in WT and Peril KO Hi-C samples. The red line indicates the distance-normalized average interaction frequency, whereas the dashed lines represent the ± 1 standard deviation. The 20-kb bins that are above the + 1 standard deviation line are considered as enriched interactions. The red arrows indicate the alterations of long-range interactions of Mccc1 and Exosc9 with the Peril locus between WT and KO samples