Figure 5

Regulation of intronic APA and C/P events around transcription start site (TSS) in response to UV. (a) Distribution of introns with activated pAs in genes. 1, first intron; 2, second intron; M, middle introns; −2, second to the last intron; −1, last intron. Single introns were excluded from this analysis. The number of introns falling into multiple types, for example, both +1 and −1 types, was evenly divided in calculation. Introns with pAs at 0 h were used as control. Changes of percent of introns with activated pAs at 0.5 vs 0 h or 2 vs 0.5 h are shown in a table next to the plot. (b) Boxplot showing distance from the transcription start site (TSS) to intronic pAs. Only the 25th to 75th percentile values are shown. The 0 h data are based on all detected intronic pAs, and the 0.5 vs 0 h and 2 vs 0.5 h data are based on activated intronic pAs. P-values were based on Wilcoxon test comparing the 0.5 vs 0 h or 2 vs 0.5 h values with those of control (0 h). (c) Distribution of pAs around the TSS. Top panel: all detected pAs in three samples are plotted, and are shown as reads per million (RPM) per base. The pAs within 4 kb from the TSS on the anti-sense strand are called upstream anti-sense RNA (uaRNA) pAs, and those within 4 kb from the TSS on the sense strand are called sense proximal RNA (spRNA) pAs. For uaRNA pAs, we discarded pAs that were associated with any known genes, and for spRNA pAs we excluded pAs that were located in the 3ʹ-most exon of genes. Bottom panel: the amounts of uaRNAs or spRNAs are shown in bar graphs. The ratio of transcript amount in the 2 h sample to that in the 0.5 h sample for spRNA pAs (top) or uaRNA pAs (bottom) is indicated. (d) Distribution of nucleotides as a function of base position around the pA identified by 3ʹREADS. The upstream and downstream regions around the pA were analyzed, spanning from −100 nt to 100 nt, with the pA set at 0 nt. The y-axis indicates frequency of each type of nucleotide at a given position. Top panel: nucleotide frequency around 3ʹUTR pAs (14 058 in total). Bottom panel: nucleotide frequency of intronic pAs (6 750 in total). APA, alternative cleavage and polyadenylation; 3′READS, 3′ region extraction and deep sequencing.