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. Author manuscript; available in PMC: 2022 Feb 2.
Published in final edited form as: Nat Aging. 2021 Aug 2;1(8):684–697. doi: 10.1038/s43587-021-00091-x

Figure 1. Age-associated increase in cryptic transcription detected in mHSC and hMSC RNA-seq data.

Figure 1.

A and B) Boxplots of the log2-transformed ratio of reads mapping to the indicated exon vs. reads mapping to the first or second exon (dark or light orange, respectively) in old vs. young samples (ratio in old divided by ratio in young, ratio of ratios), in mHSCs (A) and hMSCs (B). Expressed major transcripts with at least 3 exons were included for mHSC (n=10068) and hMSCs (n=9230). 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. Significance was determined by a two-sided Wilcoxon signed-rank test with the null hypothesis that the log2-transformed ratios are equal to 0. p-values reported in Supplementary Table 1. C) Ranked plot of CT scores for mHSCs (top) and hMSCs (bottom). The red lines show inflection points with a tangent of 1; transcripts with significantly increased CT scores, i.e., those with an age-associated increase in cryptic transcription, are located to the right of the second inflection point. D) Heatmaps of the CT scores of transcripts with age-increased cryptic transcription in mHSCs (left) and hMSCs (right). E) Metagene plot of RNA-seq read density in old (red) and young (blue) samples. mHSCs are on top; hMSCs on the bottom. F) Age-associated cryptic transcription in mHSCs (left, Car11) and hMSCs (right, IAH1), depicting mapped reads from young samples (top, blue), old samples (middle, red), and the difference (old-young, in red where reads are higher in old samples, blue in young; bottom panel). G) Metagene plots of RNA Pol II-Ser5P ChIP-seq enrichment in young and old hMSCs. The plot on the left shows enrichment among all transcripts; the one on the right shows enrichment only in transcripts identified as having increased cryptic transcription with age. H) Enrichment plots of RNA Pol II Ser5P ChIP-seq in exons with the highest CT score of transcripts with age-increased cryptic transcript and the first and second downstream exons. In all panels, Y: young; O: old; Diff: difference; enrich.: enrichment.