Fig 1: Aging affects the stability of the Pol II pausing complex rather than transcription initiation AHeatmap and intensity profiles of promoter accessibility over active enhancers in liver (n = 8,855). Read densities of merged biological replicates (n = 3–4) were normalized to 1× coverage.BRaincloud plots of changes in accessibility in aged versus young liver assessed by ATAC-seq. Raincloud plots are hybrid plots. Here, the violin and boxplots visualize the log2-fold change for all accessible genomic sites (“all”) or accessible sites overlapping promoters of tNET genes (“promoters”) or active enhancers in murine liver (“enhancers”). The dot plot highlights regions significantly changed with age in each category (FDR < 5%). The numbers in the plot denote significantly up- or downregulated regions in each category.CViolin and boxplots of Pol II density at enhancer regions (n = 8,144) as a means of quantifying eRNA production. P-values were calculated using a two-sided Wilcoxon rank-sum test. Box plots consist of the median (central line), the 25th and 75th percentiles (box) and the highest/lowest value within 1.5 * interquartile range of the box (whiskers).DWestern blots of cellular fractionations of young and aged liver samples probed with the indicated antibodies.EHeatmaps and average intensity profiles of RNA Pol II and its S2 and S5 phosphorylated forms in young and aged animals.FHeatmaps and average intensity profiles of SPT4 ChIP-seq signal at TSSs of tNET genes in young and aged animals. Data information: n = 3–4 biological replicates per age group for tNET-seq, ATAC-seq and CUT&RUN; n = 2 for ChIP-seq.