Extended Data Fig. 5: Chromatin state changes around age-increased cTSSes.

a, Read pile ups of H3K4me3 around annotated TSSs (left), age-increased cTSSs (middle), and age-decreased cTSSs (right), independently clustered into 3 groups. b, As in a, except H3K4me1 enrichment is shown. c, As in a, except depicting H3K27ac enrichment. d, Boxplots showing H3K36me3 enrichment around age-increased cTSSs (n = 1,373) and endogenous TSSs (n = 13,802) in young and old hMSCs. P values were calculated using a two-sided Wilcoxon signed-rank test with the null hypothesis that enrichment was equal in the young and old samples. e, Bar chart showing the proportion of TBP ChIP-seq peaks around endogenous TSSs in young and old hMSCs. f, Metagene plot of TBP enrichment around annotated TSSs in hMSCs. g, DECAP-seq signal around putative age-associated cTSSs predicted in hMSCs by the chromatin state model. Averaged read depth of putative age-associated promoter regions (±1 kb of the midpoint of the identified region) in young (blue) and old (red) is shown on the left at 100 bp resolution; a boxplot of the log₂-transformed ratio of signal in old vs. signal in young shown on the right (n = 166). Distinct random genic non-promoter regions (length = 2 kb) were used as control (n = 2,774). P values were calculated using a two-sided Wilcoxon signed-rank test vs. the hypothesis that the RNA-seq ratios were equal in the putative age-increased cTSSs vs. control regions, as appropriate. Regions without DECAP-seq signal were excluded from analysis. In all panels, Y: young; O: old; TSS: transcription start site; cTSS: cryptic transcription start site. For boxplots, bounds of box show the 25th and 75th percentiles; the central lines in the box plots represent the median value; and whiskers show 1.5-fold of the interquartile range.