NFI Transcription Factors Provide Chromatin Access to Maintain Stem Cell Identity While Preventing Unintended Lineage Fate Choices

Tissue homeostasis and regeneration rely upon resident stem cells (SCs), whose behavior is regulated through niche-dependent crosstalk. The mechanisms underlying SC identity are still unfolding. Here, using spatiotemporal gene ablation in murine hair follicles (HFs), we uncover a critical role for transcription factors (TFs) NFIB and NFIX in maintaining SC identity. Without NFI-TFs, SCs lose hair-regenerating capability, and produce skin bearing striking resemblance to irreversible human alopecia, which also displays reduced NFIs. Through single cell transcriptomics, ATAC-seq and ChIP-seq profiling, we expose a key role for NFIB/NFIX in governing super-enhancer maintenance of the key HF-SC specific TF genes. When NFIB/NFIX are genetically removed, the stemness epigenetic landscape is lost. Super-enhancers driving SC identity are decommissioned, while unwanted lineages are de-repressed ectopically. Together, our findings expose NFIB/NFIX as crucial rheostats of tissue homeostasis, functioning to safeguard the SC epigenome from a breach in lineage confinement that otherwise triggers irreversible tissue degeneration.