Fig. 5.

3′UTR shortening by APA leads to preservation of mRNA during stress recovery. a Schematic of experimental design. Total cellular RNA was subject to strand-specific RNA-seq to examine gene expression changes. Only reads mapped to CDS were used, which avoided the influence of 3′UTR size change on gene expression analysis. b Identification of genes with shortened 3′UTRs through APA. Genes with significant 3′UTR shortening in newly made RNAs of both AS and RC samples (shown in blue) were selected. Black dots are other genes with APA isoforms detected in NIH3T3 cells. c RNA abundance changes for three groups of genes after AS (1 h, left) or RC (4 h, right). Groups 1 and 2 genes correspond to blue and black dots in b. Group 3 genes were those without APA isoform expression in NIH3T3 cells. Gene numbers are shown in parentheses. Median log2(ratio) of gene expression level (RPM) between two conditions is shown in each graph. P-values (K–S test) indicating difference in gene expression change (RC vs. NT) between gene groups are shown