Fig. 3: Gene-length-dependent RNAPII stalling in old mouse livers.
From: Genome-wide RNA polymerase stalling shapes the transcriptome during aging
a, Three-bin heatmap of log2 fold changes (old/adult) of nascent RNA and ChIP–seq of total RNAPII on gene bodies, sorted by level of transcriptional decline on all expressed genes. b–d, Relative sequencing densities of the transcription elongation phase between TSS and TTS. b, Nascent RNA sequencing in adult (blue) and aged (red) liver. c, Total RNAPII ChIP–seq in adult (blue) and aged (red) liver. d, RNAPII-ser2p ChIP–seq in adult (blue) and aged (red) liver. All expressed genes; n = 3 mice per group. P values: unpaired two-sided t-test with 32 d.f. Data are presented as the mean ± s.e.m. e,f, Percentage sequencing read density change in the transcription elongation phase in aging between TSS and TTS of gene categories based on genomic gene length: EU-seq (e) and total RNAPII ChIP–seq (f). g, Percentage sequencing read density change (old/adult) in EU-seq as seen in Fig. 2e, in which the x axis is the average gene length of each category. h, Scatter plot depicting all expressed gene lengths >20 kb (x axis) and percentage change between old and adult in EU-seq densities from TSS to 20 kb downstream (y axis) (n = 3,308). i, Percentage stalled RNAPII in gene bodies. The colors indicate the gene-length classes as in Fig. 2e. Data are the mean ± s.d. (10–22 kb: n = 662; 22–30 kb: n = 644; 30–50 kb: n = 788; 50–70 kb: n = 587; 70–110 kb: n = 643; and >110 kb: n = 646).
