Extended Data Fig. 5: The DNAm drift expands via crypt clonality and shows heterogeneity at the CpG level.

a, The DNAm level of the Dkk1, Sfrp1, and Sfrp2 gene promoters analyzed by BS pyrosequencing in 59, 45, and 78 single crypts isolated from young and old mice, respectively (as indicated). Each circle represents the DNAm level (in percentage). The failed DNAm analysis is represented by dashes. n = 3 mice per group were analyzed. b, The DNAm level of the β-Actin (in 60 young and 72 old single crypts) and Dppa3 (in 25 young and 45 old single crypts) gene promoters analyzed by BS pyrosequencing in small intestinal crypts isolated from young and old mice. n = 3 mice per group were analyzed. p-value was calculated by Welch’s t-test 2-tails. Error bars represent the SD. c, Violin plot showing the DNAm level of the Dkk1, Sfrp1, and Sfrp2 gene promoters in single intestinal crypts isolated from young and old mice as in (a). d, Hierarchical clustering and heatmap of the Pearson correlation of the DNAm profiles of the Dkk1 gene promoter of 59 single crypts. e, The DNAm profile of the Dkk1 gene promoter in the crypts from the Cluster 1 (crypts isolated from young mice - ‘young’ crypts cluster) (left panel). The DNAm profile of the Dkk1 gene promoter in the crypts from the Cluster 5 (crypts isolated from old mice - ‘old’ crypts cluster) (right panel). f, Histogram plot showing the average DNAm level of three genes analyzed in single crypts as in (a) and Fig. 3b.