Fig. 4: Meta-analysis of methylation change in function of chronological age across species and tissues.

a–d,g,h, Eutherian EWAS of age. a, Meta-analysis −log₁₀ (P values) for age-related CpG sites (annotated by proximal genes) on chromosomes (x axis in hg38). Top and bottom, CpG sites that gain or lose methylation with age, respectively. CpG sites in red and blue denote highly significant positive and negative age correlation (P < 10⁻²⁰⁰), respectively. The most significant CpG (cg12841266, P = 1.41 × 10^−1,001) resides in exon 2 on the LHFPL4 gene in humans and most mammals, followed by cg11084334 (P = 2.59 × 10⁻⁸⁹¹). These two CpG sites and cg097720 (P = 4.97 × 10⁻⁷⁸⁷) located in the paralog gene LHFPL3 are marked with purple diamonds. b–d, Scatterplots of cg12841266 versus chronological age (years) in mini pigs (Sus scrofa minusculus) (b), Oldfield mice (Peromyscus polionotus) (c) and horses (Equus caballus) (d). Tissue samples are labeled by the mammalian species index and colored by tissue type as detailed in Supplementary Data 1.1–1.4. e,f, Correlation analysis between Z scores of EWAS of age in eutherians versus marsupials (e) and eutherians versus monotremes (f). g,h, Annotations of the top 1,000 CpG sites with increased or decreased methylation with age that were identified in EWAS meta-analysis across all species and tissues (results in a) (brain, cortex, blood, liver, muscle and skin tissues). g, The overlap of age-associated CpG sites across various organs, based on the top 1,000 CpG sites showing positive or negative age correlation in EWAS. The Venn diagram includes 51 age-associated CpG sites shared across all organs, adjacent to 38 genes (35 with positive and three with negative age correlation) categorized by protein family. The 35 positive genes are color coded based on their protein family: two in LHFPL, 12 in homeobox, three in paired box or T-box, three in bHLH, seven in zinc finger and eight in others. h, Selected universal chromatin state and polycomb group protein enrichment results. ORs (P values) are presented in each cell. The color gradient is based on −log₁₀ (hypergeometric P value) times sign of OR > 1. The complete results are listed in Extended Data Fig. 7. State annotation can be found in Supplementary Data 8.2. HET denotes heterochromatin. Except for the hypergeometric analysis in h, all figure P values are unadjusted and two sided.