Figure 2.

Genome-Wide Distribution of Poly(A) Site Usage in Response to Hypoxia.

(A) Gene expression comparison under normal and hypoxic conditions. Scatterplot comparing gene expression results from previous published studies using RNA-seq (Juntawong et al., 2014a) and from the assessment of gene expression using PAT-seq (this study). Scatterplot of the log₂-transformed expression ratios for genes present in both experiments. The correlation coefficients were calculated using the whole transcriptome (r₁) or only values with greater than 2-fold change (r₂) from both experiments.

(B) Box plots showing change in usage of different classes of poly(A) sites. For this, the relative contribution that each PAC makes to total poly(A) usage was determined on a gene-by-gene basis, with the ratios of usage in hypoxic and control plants calculated and log₂-transformed. “Gene” represents the complete collection of PACs. Vertically oriented numbers near the top indicate the total number of PACs in each class.

(C) Percentage of upregulated and downregulated mRNA isoforms. Values > 2× or < 0.5× of PAC/gene normalized fraction with respect to the control are indicative of more or less relative poly(A) cluster usage, respectively. Statistically significant values were determined using the hypergeometric probability (P value < 0.0001, comparison between 2-fold change usage in a specific isoforms with the overall of the same isoform) and are denoted with asterisks (detailed statistic archived in Supplemental Data Set 4).

(D) Ontology term enrichment according to the BAR Arabidopsis website (http://bar.utoronto.ca/). Only ontology terms significantly enriched were included (P value < 0.01 and 1.5-fold). The purple scale shows the bootstrap values.

(E) Box plots showing changes in overall expression of genes possessing different classes of poly(A) sites, as described in the text. For each gene, the log₂-transformed fold change in expression in hypoxic plants was extracted from the data set described (Juntawong et al., 2014a); the bulk values for each class were then presented as shown. “Multiple locations” denotes genes with noncanonical poly(A) sites that lie within more than one genomic location. FC, fold change; r, correlation coefficient; T, total RNA; NS, normal conditions; HS, hypoxic conditions. PACs defined by fewer than 10 PATs in the study were excluded from the analysis.