Unequal distribution of RNAPIII along tRNA genes indicated by genome-wide analysis. (A) Cumulative plot of all nuclear tRNA genes aligned to the mature 5′-ends. Distance (nt) is shown starting 200 nt upstream of the mature 5′-ends (designated by vertical green line) on the x-axis. (B) Cumulative plot aligned to 3′-ends of mature tRNAs (designated by vertical red line). (C) Hit distribution along individual genes [tA(AGC)K2, tF(GAA)G, tW(CCA)M], showing uneven patterns of RNAPIII occupancy. The x-axis shows distance (nt) from the 5′-end of the mature tRNA. The light green background indicates the exonic region(s). The area filled in blue represents RNAPIII read-through of the canonical termination signal. Plots for all tRNA genes are presented in Supplemental Data Set D1. (D) Heatmap for all nuclear tRNA genes with 50-nt 5′ flanks and 150-nt 3′ flanks, clustered using the 1-Pearson coefficient. The hit intensity scale is shown relative to the maximum value within each gene. The 5′ peak is the predominant feature. (E) All nuclear tRNA genes were ordered according to 5′ to 3′ peak ratios. The color intensity compares the number of reads to the global distribution of mapped reads. (F) Genome-wide profile of 225 tRNA genes aligned to 5′-ends of mature tRNAs. These genes (group 1) show the predominant pattern with a higher 5′ peak (5′ to 3′ peak ratio >1.5). (G) Genome-wide profile of the remaining 50 tRNA genes (group 2) showing the less common pattern with similar-sized 5′ and 3′ peaks (5′ to 3′ peak ratio <1.5). (H) Genome-wide profile of all nuclear tRNA genes aligned to A box. The start of the A box sequence is indicated by a vertical line. (I) Profile aligned to B box. The start of the B box sequence is indicated by vertical line.
