Fetal myogenesis chromatin state and CpG from the open alliance markers and their intersection with adult muscle and gastrointestinal genetics.

BACKGROUND

Epigenetic inheritance links fetal chromatin organization and CpG methylation to lifelong tissue phenotypes. We tested the Fetal Chromatin-CpG Developmental Blueprint (FCCD-B) model, proposing that fetal chromatin states shaped by maternal nutrient and transcription factor networks establish regulatory programs preserved in adult traits.

METHODS

We integrated 21 970 fetal single-cell transcriptomes with chromatin accessibility data, including 130 myogenic cells. Adult GWAS datasets included 1614 appendicular lean mass (ALM) loci and 445 grip strength loci. Fine-mapping, colocalization, and gene regulatory networks were inferred using GRNBoost2, Enformer, and Basenji, alongside virtual-cell simulations of nutrient and stress perturbations.

RESULTS

ALM and grip strength showed strong genetic correlation (rg = 0.49; Z = 26). Fine-mapping identified 1355 high-confidence ALM loci (median PIP = 0.91). A total of 2935 shared GWAS-eQTL variants overlapped fetal chromatin, with 70-88% accessibility preserved in endothelial and cardiomyocyte lineages. A SMAD3-centered TGF-β network (50 targets) was identified. Simulations showed that vitamin D, folate, and oxidative stress increased myofibril index (+0.141), epithelial regeneration (+0.035), and combined effects (+0.147).

CONCLUSION

Persistent fetal chromatin and CpG architectures encode regulatory programs linking maternal environment to adult phenotypes, supporting the FCCD-B model as a predictive framework for developmental epigenetics.