Transcription factors induce different stem cell states through distinct pioneer, collaborative and competitive interactions

Abstract

Cell fate conversion requires the action of groups of transcription factors (TFs), but the underlying principles remain elusive. Here, I investigated how four TF combinations lead to different reprogramming outputs. Pioneer TFs initiate reprogramming through OFF-target binding to closed chromatin which becomes accessible only when targeted by multiple TFs. After reprogramming completion, TFs are co-bound within accessible chromatin, with limited binding to closed chromatin by individual pioneer TFs. Pioneer TFs access distinct nucleosome conformations including mono-nucleosomes or nucleosome-arrays embedded in closed chromatin and fragile-nucleosomes laced throughout accessible chromatin. On the nucleosome each pioneer TF displays a distinct positional binding preference relative to the nucleosome dyad which changes between early and final reprogramming. Interestingly, the ability of pioneer TFs to direct non-pioneers to closed chromatin is markedly different across reprogramming systems. Competitive interactions expand reprogramming capacity by depleting loosely bound TF interactions with the genome without repositioning. These findings uncover distinct modes of action for TFs during cell fate determination.