Synchronizing donor cells to early S‑phase reduces replication‑timing‑driven epigenetic noise and improves iPSC rejuvenation

Hypothesis: Heterogeneity in replication timing during OKSM‑induced reprogramming creates epigenetic noise that blocks complete erasure of late‑replicating heterochromatic marks, thereby limiting rejuvenation. Transient synchronization of donor fibroblasts into early S‑phase before OSK expression will align chromatin opening events with peak OSK factor activity, producing more uniform euchromatin remodeling, faster dilution of residual H3K9me3/H3K27me3, and a steadier decline in epigenetic age.

Mechanistic rationale: Replication forks convey epigenetic information via histone chaperone deposition and DNA methyltransferase activity. Early‑replicating euchromatin is preferentially accessed by OSK factors, while late‑replicating heterochromatin is refractory due to delayed fork arrival and tighter nucleosome packing. By enriching cells in early S‑phase (e.g., double thymidine block), we increase the proportion of loci that are replicating when OSK levels rise, reducing the stochastic mismatch between factor binding and replication‑coupled chromatin opening. This should lower cell‑to‑cell variance in accessibility at OSK‑bound sites (epigenetic noise) and allow histone modifications that resist dilution (e.g., H3K9me3) to be more efficiently diluted over successive divisions.

Testable predictions: (1) Synchronized cells will show reduced scATAC‑seq variance at OSK‑bound enhancers compared with asynchronous controls at 6‑12 h post‑induction. (2) Repli‑ATAC‑seq will reveal increased concordance between early replication timing and OSK‑induced accessibility peaks. (3) Across passages 2, 5, and 10, DNA methylation age (Horvath clock) will decline more rapidly and reach lower plateau values in synchronized iPSCs. (4) Residual H3K9me3/H3K27me3 levels measured by CUT&Tag will be significantly lower in synchronized lines. (5) Differentiation bias toward the donor fibroblast lineage (quantified by lineage‑specific marker expression after directed neuroectoderm and mesoderm induction) will be diminished.

Experimental design: Obtain fibroblasts from donors >65 years old. Split into two groups: (A) double thymidine block (2 h) followed by release to enrich early S‑phase; (B) untreated control. Induce OKSM via doxycycline‑inducible cassette. Collect samples at 0, 6, 12, 24, 48 h for repli‑ATAC‑seq and scATAC‑seq. Expand iPSCs to passages 2, 5, 10; assess DNA methylation age, H3K9me3/H3K27me3 (CUT&Tag), karyotype stability, and apoptosis (Annexin V). Perform directed differentiation assays and quantify lineage markers by flow cytometry.

Falsification criteria: If synchronization fails to reduce scATAC‑seq variance, does not accelerate epigenetic age decline, or does not lower residual heterochromatic marks despite verified S‑phase enrichment, the hypothesis is falsified. Alternative explanations (e.g., toxicity from block, cell‑cycle‑independent mechanisms) would be investigated by parallel CDK2 inhibition experiments that lengthen S‑phase without blockage.

This approach directly links replication timing heterogeneity to epigenetic noise and offers a concrete, falsifiable strategy to approach complete rejuvenation of iPSCs from aged donors.