Fig. 1: Reduced RNA synthesis and increased RNAPII levels in aged liver.
From: Genome-wide RNA polymerase stalling shapes the transcriptome during aging
a, EU-labeled nascent RNA (green) in hepatocyte nuclei (DAPI counterstain, blue) in adult (blue) and old mouse liver (red). Right, Fluorescence intensities quantified in box and whisker plots. The center lines show the medians, the box limits mark the IQR, and the whiskers indicate the minimum and maximum values. P = 2.1129 × 10−129 (two-sided unpaired t-test). Counted nuclei: adult n = 506; old n = 500; n = 3 mice per group. b, XY scatterplot of fluorescence intensity of EU-labeled nascent RNA (arbitrary units (a.u.)) and corresponding nuclear sizes measured in individual hepatocytes of WT adult (blue) and old (red) liver. c–e, Total RNAPII (c), RNAPII phosphorylated at ser5p (d) and RNAPII phosphorylated at ser2p (e) immunofluorescence staining (red) in hepatocytes (counterstained by DAPI, blue) in adult and old liver. Box and whisker plots of fluorescence intensities. The center lines show the medians, the box limits mark the IQR, and the whiskers indicate the minimum and maximum values. P values by two-sided unpaired t-test, n = 3 mice per group. Counted nuclei and P values: c, adult: n = 206; old: n = 155, P = 6.64186 × 10−21; d, adult n = 2,926; old n = 2,643, P = 0.323195587; e, adult n = 2,697; old n = 2,708. P = 0. Scale bar, 50 μm. f, Flow chart of the experimental procedure for EU-labeled nascent RNA sequencing. g, Fraction (%) of EU-seq reads synthesized by different RNA polymerases. RNAPI–II and mtRNAP (left) and RNAPIII (right), with total sequence reads of adult and old normalized to 100%. Data are the mean ± s.e.m. n = 3 mice per group. P = 0.012868073 (two-sided unpaired t-test). h, Fraction (%) of EU-seq reads by RNAPII from intronic and exonic regions. Data are the mean ± s.e.m. n = 3 mice per group. P = 0.013520897 (two-sided unpaired t-test).
