Figure 1. Poly(A) sites are shifted upstream in diauxic cells.

(A) Representative end zone profile (histogram of isoform frequencies) with key landmarks indicated. (B) End zone profiles for four genes under five growth conditions. (C) Major end zone under five growth conditions. Boundaries represent median values genome-wide for 5’-most and 3’-most major isoforms, and the vertical line within the major end zone represents the genome-wide median of the weighted average isoform position. (D) Table of statistics for landmark positions under five growth conditions. Numbers are the median values across genes with a combined read count of at least 1000 in both replicates in every condition. Numbers in bold red are shifted upstream from WT in a statistically meaningful way (p < 0.01).

Figure 1—figure supplement 1. Correlation of biological replicates.

(A) Correlation of reads per gene in two biological replicates. Each plot shows all genes with ≥1000 reads in the two conditions (>5000 genes/plot). (B) Correlation of reads per isoform in two biological replicates. The plot for each condition shows 25,000–75,000 isoforms. Isoforms with fewer than 10 reads were omitted. (C) Correlations of overall isoform profiles across biological replicates. Pearson correlations were determined for isoform profiles of the 2790 genes with ≥1000 total reads (in both replicates combined) in every experimental condition. Left: Distribution of isoform profile correlations for genes in every condition. Right: Genome-wide median correlations of isoform profiles across biological replicates. (D) Heat map of 3’UTR coordinate use in five growth conditions. For every condition, the heat map depicts the fraction of genes in the genome for which each 3’ UTR position is used as a poly(A) site. In this plot, the relative use of poly(A) sites at individual genes is not considered; rather, the result for a given position at any gene’s 3’ UTR is binary. A position is counted as positive for the gene if any isoform endpoints map there.