Fig. 5: Transfer RNA gene body and upstream sequences govern differential Pol III recruitment.
From: Selective gene expression maintains human tRNA anticodon pools during differentiation
a, Representative heatmaps (bottom) and metagene profiles (top) of the ChIP–Seq signal for RPC1, H3K4me3 (K4me3), H3K27me3 (K27me3), H3K9me3 (K9me3) and NFRs from ATAC–Seq around tRNA gene start sites (±1 kbp) for hiPSC and neurons, separated by tRNA gene activity. b, Distances between tRNA genes from different activity classes to their nearest tRNA gene. Box plots: centre line, median; box limits, upper and lower quartiles; whiskers, 1.5× the interquartile range. c, Relationship between RPC1 occupancy at tRNA genes (mean from n = 2 biological replicates) and the predicted tRNAScan-SE score, separated by tRNA gene activity. Dashed lines, median tRNAScan-SE score and RPC1 occupancy; solid blue line, 55-bit score tRNAScan-SE threshold for functional tRNAs. d, Two-dimensional binned kernel motif density of the A (left) and B (right) box of each tRNA gene (n = 558) separated by tRNA activity (centre line, median). Motif counts for density estimation were based on a 90% match to the consensus motif. Dot colour is used to indicate whether the tRNAScan-SE score is above or below the 55-bit threshold for predicted functionality (Wilcoxon test). e, Schematic of CRISPR–Cas9 editing to replace tRNA-Pro-TGG-2-1 with tRNA-Pro-TGG-1-1 (left). Fraction of tRNA-mapped RPC1 ChIP–Seq reads at wild-type and CRISPR-edited hiPSC and NPC (n = 2 biological replicates for each cell type; bar, median) at the indicated tRNA genes. f, Receiver operating characteristic for tRNet performance on test data for each task. g, Top three significant TF-Modisco sequence motifs (FDR-adjusted P ≤ 0.01) for housekeeping tRNA genes. h, Schematic of CRISPR–Cas9 editing to insert the 100-bp sequence upstream of tRNA-Pro-TGG-1-1 in front of tRNA-Pro-TGG-2-1 (left). Fraction of tRNA-mapped RPC1 ChIP–Seq reads at wild-type (data from e) and CRISPR-edited hiPSC and NPC (n = 2 biological replicates; bar, median) at the indicated tRNA genes (right). i, Mean expression of CADM3 in RNA-Seq datasets across cell types (n = 2 biological replicates). j, Representative plot of normalized ChIP–Seq signal for RPC1 ChIP, K4me3 ChIP and RNA-Seq signal surrounding the tRNA-Arg-TCT-4-1 and CADM3 genes in hiPSC and NPC as well as neurons. WT, wild-type; edit, CRISPR-edited. Source numerical data are provided.
