Extended Data Fig. 4: The ACCA drift is cell-intrinsic and cell-cycle independent.

a, DNAm level of the Sfrp1 gene promoter in the different tissues at the indicated ages. n = 3 mice per group were analyzed. b, Schematic representation of the experimental set up. c, Bar chart indicating the DNAm level of the Dkk2 and Sfrp1 gene promoter analyzed by BS pyrosequencing in small intestinal (SI) and colon crypts and organoids at the indicated ages. n = 3 mice per group were analyzed. d, Bar chart indicating the DNAm level of the Dkk2 gene promoter analyzed by BS pyrosequencing upon long-term organoid culture of crypts isolated from young and old mice. n = 3 mice per group were analyzed. p-value was calculated by an unpaired t-test, 2-tails. e, Bar chart showing the DNAm level of the Sfrp1 gene promoter upon long-term organoid culture of crypts isolated from young and old mice. n = 3 mice per group were analyzed. p-value was calculated by an unpaired t-test, 2-tails. f, Boxplot indicating the DNAm level of the ACCA drift gene promoters in intestinal crypts isolated from young, old, and geriatric mice. For each age group, values are shown separately for female (1 F, 2 F, 3 F) and male (1 M, 2 M, 3 M) mice. n = 4 mice per group were analyzed. p-value was calculated by paired t-test, 2-tails. Box plots represent interquartile range with 5-95 percentile whiskers. g, Boxplot indicating the DNAm level of the ACCA drift gene promoters measured by RRBS upon long-term organoid culture of crypts isolated from young mice. n = 2 mice were analyzed. p-value was calculated by paired t-test, 2-tails. Box plots represent interquartile range with 5-95 percentile whiskers. h, Bar chart showing the DNAm level of the Sfrp1 gene promoter upon 1 month of organoid culture of crypts isolated from young and old mice and cultured in the indicated conditions. n = 3 mice per group were analyzed. p-value was calculated by an unpaired t-test, 2-tails. i, Bar chart indicating the DNAm level of the Sfrp1 gene promoter analyzed by BS pyrosequencing upon 1 month of organoid culture of crypts isolated from young mice and cultured in the indicated conditions as in Fig. 2l. n = 3 mice per group were analyzed. p-value was calculated by an unpaired t-test, 2-tails. j, Bar chart showing the DNAm level of the Sfrp1 gene promoter upon 1 month of organoid culture of crypts isolated from young and old mice and cultured in the presence of CHIR99021 or recombinant Wnt3a. n = 3 mice per group were analyzed. p-value was calculated by an unpaired t-test, 2-tails. Error bars in the figure bar charts represent the SD.