Extended Data Fig. 3: The ACCA drift is conserved in the mouse intestine and originates at the stem cell level.
a, Scatter plot of the delta methylation (old minus young) on all the CpG islands in the Lgr5hi cells and whole crypts. Linear regression was performed (lm function in R), and statistical significance of regression coefficients was assessed using two-sided t-tests; overall model fit was evaluated using an F-test (F-statistic: 4.27 × 10⁴). The p-value for the slope was obtained as twice the probability of observing a t statistic as extreme as 206.65 under a Student’s t distribution with 12419 degrees of freedom. Because this value is far smaller than machine precision, the exact p-value cannot be reported and is conventionally written as p < 2.2 × 10⁻¹⁶. b, Venn diagrams of the DM CpG islands found in the Lgr5hi cells and whole crypts. p-value was calculated by a one-sided hypergeometric distribution test. The computed probability of observing an overlap, given the background of 12,421 CpG islands, is far smaller than machine precision thus exact p-value cannot be reported due to numerical underflow in the calculation. c, Genomic views of the Dkk2 and Sfrp1 gene promoters showing the DNAm level in young and old Lgr5Hi ISCs. Each line is a replicate. Each rectangle is a CpG. d, Scatter plot of the average DNAm level of the ACCA drift genes and of the two marker genes DKK2 and SFRP1 (upper panel) or of the 4 marker genes DKK1, DKK2, SFRP1, SFRP2 (lower panel) in colon cancer samples. The gray line indicates linear regression; the shaded area represents the 95% confidence interval. e, Correlation coefficients between the average DNAm level of the ACCA drift genes and 100 random groups of either two (left panel) or four genes (right panel). The correlation coefficient with the average DNAm level of the two selected marker genes DKK2 & SFRP1 or four selected marker genes DKK1, DKK2, SFRP1, and SFRP2 is also shown, respectively.
