AP-1-driven chromatin erosion as a conserved aging mechanism in stem cells

Hypothesis: Chronic AP-1 activation, fueled by low‑grade TNF signaling, reprograms the chromatin landscape of aged stem cells by simultaneously eradicating accessibility at identity‑maintaining enhancers and creating de novo open regions at stress‑response promoters. This occurs because AP-1 heterodimers (c‑Jun/FosB) recruit histone acetyltransferases (p300/CBP) and displace nucleosome‑remodeling complexes that normally preserve repressive H3K9me3 marks at lineage‑specific loci. The resulting loss of MEF2‑bound enhancers in neural stem cells and gain of CEBP‑driven myeloid motifs in hematopoietic stem cells are two sides of the same AP‑1‑centric rewiring. Restoring DMTF1 competes for AP‑1 binding sites and recruits the NuRD complex, re‑establishing H3K9me3 at eroded enhancers while closing ectopic AP‑1‑driven openings, thereby rescuing quiescence and differentiation capacity.

Predictions:

1. In aged neural and hematopoietic stem cells, pharmacologic inhibition of AP‑1 (e.g., T-5224) or genetic knockout of c‑Jun will prevent age‑dependent loss of MEF2 motifs and gain of CEBP motifs, as measured by sci‑ATAC‑seq.
2. Concurrent CUT&RUN for H3K27ac and H3K9me3 will show that AP‑1‑bound gains correlate with increased H3K27ac and decreased H3K9me3 at former MEF2 sites, whereas AP‑1‑bound losses show the opposite pattern.
3. Overexpression of DMTF1 in aged stem cells will reduce AP‑1 occupancy at ectopic sites (ChIP‑seq) and restore the original accessibility profile without altering TNF levels.
4. Longitudinal sci‑ATAC‑seq of murine intestinal crypt stem cells and muscle satellite cells will reveal the same AP‑1‑motif swap, indicating a conserved mechanism beyond the neural and hematopoietic systems.
5. Human single‑cell ATAC‑seq from aged donors will show enrichment of AP‑1 motifs in regions that lose accessibility in young donors, and TNF blockade in vitro will diminish these changes.

Falsification: If AP‑1 inhibition fails to rescue identity‑element accessibility or if DMTF1 overexpression does not alter AP‑1 binding or chromatin states, the hypothesis would be refuted, suggesting that other transcription factors or independent epigenetic drift drive the observed remodeling.