Extended Data Fig. 4: Genome-wide analysis of chromatin states.

a, Emission parameters of the ten state ChromHMM model in hMSCs. b, Enrichment of the ChromHMM states in the indicated genomic regions in young hMSCs. c, As b, except in old hMSCs. d, Enrichment of the ChromHMM states around annotated TSSs and TESs in young and old hMSCs. e, Transition map of ChromHMM states in old vs. young hMSCs. State in old is along the x-axis and state in young along the y-axis. f, Two examples of a decline in H3K9me3 (ChromHMM state 1) enrichment at LADs with age. Normalized mapped reads are shown in blue for young hMSCs and in red for old. g, Distribution of the chromatin states of age-decreased cTSSs determined by DECAP-seq in young and old hMSCs. h, Methylated CpG distributions in young (left) and old (right) hMSCs. i, Number of CMS-IP-seq (5-hydroxymethylcytosine) peaks in young and old hMSCs. j, Graphical representation of a one-sided permutation test with the null hypothesis that the number of CMS-IP-seq peaks that overlap with age-increased DECAP-seq peaks is equal to the background level of CMS-IP-peaks. This shows a significant overlap of CMS-IP-seq peaks with age-increased cTSSes. In all panels, Y: young; O: old; TSS: transcription start site; TES: transcription end site; LAD: lamin-associated domain.