Chromatin interaction profiles at bivalent genes by multiplexed splinkerette 4C sequencing

To examine chromatin interaction profiles around bivalent gene loci, we developed a multiplexed splinkerette Chromosome Conformation Capture Combined with high-throughput sequencing (ms4C-seq). By using ms4C-seq, we showed that bivalent gene loci tend to be colocalized in hiPSCs and that the colocalization requires PRC1, PRC2 and TrxG complexes that are the essential regulatory factors for maintenance of developmental genes in the transcriptionally poised state. Examination of chromatin interaction profiles for 89 bait loci on human iPSCs, and for 42 bait loci out of 89 bait loci on their original HFs, and those at 8 gene loci for hiPSC treated with shRNA against EED, WDR5 and RING1B. All experiments were performed in biological replicates.