Figure 2: Enhancer reorganization during reprogramming is linked to distinct TF binding and motif patterns.

A) Key enhancer and associated TF binding changes during reprogramming. Very early in reprogramming, OSK bind a fraction of somatic enhancers as well as transient enhancers and a subset of pluripotency enhancers. At transient and early-engaged pluripotency enhancers, OSK co-bind with somatic TFs. Over time, early engaged pluripotency enhancers gain the binding of additional TFs throughout reprogramming (such as NANOG), which replaces the binding of somatic TFs. The majority of pluripotency enhancers is engaged later in the process (late-engaged) by O and S (without K) and requires additional TFs (for instance ESRRB) that are activated during the reprogramming process. In starting fibroblasts, both early and late-engaged pluripotency enhancers lack hypersensitivity (based on ATAC-seq) and reprogramming factor binding coincides with substantial nucleosome removal. Based on the presence and absence of DNA sequence motifs (as shown on the right), it is thought that OSK engage transient and pluripotency enhancers through direct DNA binding and interact with somatic enhancers largely indirectly.

B) Somatic TF redistribution model. Early in reprogramming, OSK recruit broadly expressed somatic TFs such as AP-1, CEBP, TEAD (orange symbols) to new sites in transient and pluripotency enhancers, depleting them from somatic enhancers. Since somatic cell-specific TF occupancy at somatic enhancers depends on the presence of broadly expressed somatic TFs, the binding of somatic cell-specific TFs (yellow symbols) is also decreased in this process. The redistribution of broad somatic TFs and the loss of somatic cell-specific TFs lead to the destabilization of fibroblast enhancers and the repression of the somatic gene program. In this model, OSK inactivate somatic enhancers indirectly, without the need for direct binding to somatic enhancers.

C) Putative roles for somatic TF binding at early-engaged pluripotency enhancers. From left to right: broadly expressed somatic TFs may collaborate with OSK to remove nucleosomes if their binding sites are within one nucleosome length, and therefore be required for enhancer opening early in reprogramming; somatic TFs passively bind to DNA in regions opened by OSK; and somatic TFs indirectly bind through protein-protein interaction with OSK or co-factors. In the latter two cases, somatic TFs may not have a specific function or, alternatively, may block the activation of these enhancers.