Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ATAC-seq]

Ectopic expression of selected transcription factors enables reprogramming of somatic cells to pluripotency. Despite steady progress in the field the exact molecular mechanisms that coordinate this remarkable transition remain still largely elusive. To better understand the final steps during the acquisition of pluripotency, we optimized an experimental system where cells exit pluripotency and then are systematically challenged to reacquire pluripotency. Using this approach we identify a transient period of deterministic reprogramming during which cells exposed to ectopic transcription factors, but not serum/LIF alone, revert to pluripotency with near 100% efficiency before approaching somatic kinetics (1-2 weeks) and efficiencies (1-2%). Investigation of the transient phase reveals unique molecular dynamics that point to a set of cis-regulatory elements that appear central to facilitating reprogramming. Interestingly, these regions retain an epigenetic signature during in vitro and in vivo differentiation and may act as primary targets of ectopically induced factors during somatic cell reprogramming. In order to better understand reacquisition of pluripotency, we designed an experimental system where differentiation iPSC are systematically challenged to reacquire pluripotency. We performed a comprehensive characterization of differentiation and reacquisition trajectories by RNA-seq,ATAC-seq and ChIP-seq for selected histone modifications.