Detailed genomic contact maps have revealed that chromosomes are composed of developmentally stable topologically associated domains (TADs) and more flexible sub-TADs. These domains reside in active and inactive nuclear compartments, but cause and consequence of compartmentalization are largely unknown. Here, we combined lacO/lacR binding platforms with allele-specific 4C technologies to track their precise position in the three-dimensional genome upon recruitment of NANOG, SUV39H1 or EZH2. We observed locked genomic loci resistant to spatial repositioning and unlocked loci that could be repositioned to different nuclear sub-compartments with distinct chromatin signatures. Focal protein recruitment caused the entire sub- TAD, but not surrounding regions, to engage in new genomic contacts. Compartment switching was uncoupled from gene expression changes and enzymatically modifying histones per se was insufficient for repositioning. Collectively this suggests that transassociated factors determine three-dimensional compartmentalization independent of their cis-effect on local chromatin composition and activity.
4C-seq was performed on a range of viewpoints in 129/Sv;C57BL/6 embryonic stem cells carying a lacO array in chromosome 8 and 11.