Intrachromosomal Looping Is Required for Activation of Endogenous Pluripotency Genes during Reprogramming

Generation of induced pluripotent stem cells (iPSCs) by defined factors is an extremely inefficient process, because there is a strong epigenetic block preventing cells from achieving pluripotency. Here we report that virally expressed factors bound to the promoters of their target genes to the same extent in both iPSCs and unreprogrammed cells (URCs). However, expression of endogenous pluripotentcy genes was observed only in iPSCs. Comparison of local chromatin structure of the OCT4 locus revealed that there was a cohesin-complex-mediated intrachromosomal loop that juxtaposes a downstream enhancer to the gene’s promoter, enabling activation of endogenous stemness genes. None of these long-range interactions were observed in URCs. Knockdown of the cohesin-complex gene SMC1 by RNAi abolished the intrachromosomal interaction and affected pluripotency. These findings highlight the importance of the SMC1-orchestrated intrachromosomal loop as a critical epigenetic barrier to the induction of pluripotency. [Display omitted] •Reprogramming factors initially bind pluripotency genes but cannot activate them•Intrachromosomal loops are required for activating endogenous pluripotency genes•The OCT4 enhancer-promoter intrachromosomal loop is orchestrated by SMC1/cohesin•SMC1 knockdown abolishes intrachromosomal loops and affects pluripotency Activation of endogenous pluripotency genes requires formation of cohesion-complex-mediated intrachromosomal loops during reprogramming and in ESCs, suggesting an epigenetic barrier that must be overcome for inducing and maintaining pluripotency.