Long-range chromatin contacts reveal a role for the pluripotency and Polycomb networks in genome organization

The spatial organization of the genome is linked to its biological function. However, the relationship between specific gene regulatory networks that govern cell identity and large-scale organization of genomes remains unclear. To investigate the basis of distal chromatin interactions occurring between genomic regions mega-bases away on the same or different chromosomes, we mapped long-range chromatin interactions in embryonic stem cells (ESCs) using 4C-seq, and examined the genomic features of the interacting regions. Confirming previous results, we show that open, accessible versus closed chromatin character is the primary determinant of distal chromatin interaction preferences, where interacting regions exhibit very similar open/closed chromatin character. We extend these results by demonstrating that genomic regions highly enriched for binding by the pluripotency transcription factors Oct4, Sox2, and Nanog preferentially co-localize, as do regions strongly enriched for Polycomb proteins and trimethylation of histone H3 at lysine 27 (H3K27me3), which include the Hox clusters. Consistent with a spatial segregation of these transcriptional networks, we find that Nanog and Polycomb proteins occupy distinct spaces in the nucleus. Importantly, loss of the Polycomb protein Eed and H3K27me3 diminishes the preferential interactions between regions normally highly enriched for Polycomb proteins and H3K27me3 without dramatically changing long-range chromatin interactions related to the open/closed chromatin state. Finally, a comparison of interactomes in ESCs and fibroblasts uncovered an ESC-specific spatial organization to the mouse genome that is gradually re-established upon reprogramming to induced pluripotent stem cells (iPSCs). Together, our data suggest that transcriptional networks that govern ESC identity play a role in determining genome-organization. We propose the existence of a hierarchy in the organization of chromatin contacts wherein, at the largest scale, the open/closed chromatin character defines an interaction space and overall chromosome conformation; on a finer scale, cell type-specific transcriptional networks direct preferential distal interactions, which we speculate are critical for efficient regulation of transcription and establishment of local chromatin environments