Mechanistic basis of lineage restriction

Lineage restriction, the biological phenomenon whereby developing cells progressively lose fate potency for all but their adopted lineages, is foundational to multicellular lifeforms as it secures the functional identities of the myriad cell types in the body. The mechanisms of lineage restriction remain enigmatic. We previously defined occlusion as a mode of gene silencing wherein affected genes lack the transcriptional potency to be activated by their cognate transcription factors (TFs). Here, we present a comprehensive mechanistic basis of lineage restriction as driven by gene occlusion. Specifically, we show that genes can become occluded simply by the default action of chromatinization in the absence of TF binding, that naive pluripotent stem cells establish full developmental potency via their capacity to erase occlusion, that primed pluripotent cells shut down this deocclusion ability in preparation for differentiation, that differentiating cells become increasingly restricted in their fate potency by the irreversible occlusion of lineage-inappropriate genes, and that stem cells employ placeholder factors (PFs) to protect silent genes needed for later activation from premature occlusion. Collectively, these mechanisms drive lineage restriction whereby the transcriptionally potent portion of the genome shrinks progressively during differentiation, rendering the fate potency of developing cells to also dwindle progressively.