Extended Data Fig. 1: A data storage chromosome lacking evolutionary history produces abundant and heterogenous transcripts in yeast.
From: Regulatory activity is the default DNA state in eukaryotes
(a) Genome browser shot of 22 kb of the data carrying chromosome expressed in yeast. Blue = sense transcription; red = antisense transcription (both log scale), with predicted transcripts indicated (red and blue). One representative replicate is shown. (b) Boxplot of lengths (y-axes) for evolved and naïve transcripts (x-axes and colours). Transcript mean lengths are longer in naïve vs evolved DNA (2-sided Wilcoxon rank sum, rep 1 p = 1.8 × 10−24, rep 2 p = 5.3 × 10−16, rep 3 p = 3.4 × 10−27) (c) Boxplot of expression levels (FPKM; y-axis) for evolved and naïve transcripts (x-axes and colours). Transcript mean FPKM is higher for evolved DNA (2-sided Wilcoxon rank sum, rep 1 p = 1.3 × 10−12, rep 2 p = 6.9 × 10−11, rep 3 p = 2.90 × 10−16). (d) Contour plot showing expression on one strand relative to the other (x- and y-axes) for evolved (upper left triangle) and naïve (lower right triangle) DNA. For (B-D), replicates (three separate RNA-seq experiments from the same yeast strain) are shown as subplots. For (B,C), n = total number of predicted transcripts for evolved or naïve DNA for each indicated replicate. Box limits = 25th and 75th percentiles; centre line = median; whiskers = farthest value within 1.5x interquartile range; points = outliers.
