We mapped long-range chromatin interactions in embryonic stem cells (ESCs), iPSCs, and fibroblasts, and uncovered an ESC-specific genome organization that is gradually re-established during reprogramming. Confirming previous results, we show that open, accessible and closed chromatin character is the primary determinant of long-range chromatin interaction preferences. Importantly, we find that in ESCs, genomic regions extensively occupied by the pluripotency factors Oct4, Sox2, and Nanog preferentially co-localize. Similarly, regions strongly enriched for Polycomb-proteins and H3K27me3 frequently interact, and loss of the Polycomb-protein Eed diminishes these interactions without dramatically changing overall chromosome-conformation. Consistent with a spatial segregation of transcriptional networks in ESCs, Nanog and Polycomb-proteins occupy distinct nuclear spaces. Together, our data reveal that transcriptional networks that govern ESC identity play a role in genome-organization.
4C-seq was performed using a variety of baits on range of mouse cell lines, namely, ESCs, reprogrammed iPSCs, partially reprogrammed pre-iPSCs, and differentiated MEFs. Additionally, 4C-seq was performed on a partially overlapping set of baits for a Eed mutant mouse ESC line and a sibling wild-type ESC line.