Virtual 4C analysis

To visualize interactions between one genomic region (viewpoint) and all other genomic sites, relevant bins were extracted from a 20-kb or 50-kb Hi-C matrix. An average interaction value for every genomic bin was calculated if the viewpoint regions spanned more than one bin. The coordinates that define the different viewpoints used in this study are shown in Supplementary Information sheet 2. To determine the relative interaction frequency of a viewpoint with chromosome cores and subtelomeres, the average interaction frequency of the viewpoint with each chromosome core and subtelomere was calculated based on the relative interaction frequencies extracted by virtual 4C analysis. The ratio between the average interaction frequency (core) and the average interaction frequency (subtelomeres) was calculated for each chromosome and plotted as one dot. The virtual 4C analysis has been implemented using HiC sunt dracones (https://doi.org/10.5281/zenodo.3570496). All scripts necessary to reproduce the Hi-C analyses can be found at: https://github.com/bgbrink/PRJEB35632.