Summary
Oct4, Sox2, Klf4, and cMyc (OSKM) reprogram somatic cells to pluripotency. To gain a mechanistic understanding of their function, we mapped OSKM-binding, stage-specific transcription-factors (TFs), and chromatin-states in discrete reprogramming stages and performed loss- and gain-of-function experiments. We found that OSK predominantly bind active somatic-enhancers early in reprogramming and immediately initiate their inactivation genome-wide by inducing the redistribution of somatic TFs away from somatic-enhancers to sites elsewhere engaged by OSK, recruiting Hdac1, and repressing the somatic-TF Fra1. Pluripotency-enhancer selection is a step-wise process that also begins early in reprogramming through collaborative binding of OSK at sites with high OSK-motif density. Most pluripotency-enhancers are selected later and require OS and other pluripotency TFs. Somatic and pluripotency-TFs modulate reprogramming efficiency when overexpressed by altering OSK-targeting, somatic-enhancer inactivation, and pluripotency-enhancer selection. Together, our data indicate that collaborative interactions among OSK and with stage-specific-TFs direct both somatic-enhancer inactivation and pluripotency-enhancer selection to drive reprogramming.