Fig. 4: Differentiation restricts Pol III to a housekeeping tRNA gene set encoding major isodecoders.
From: Selective gene expression maintains human tRNA anticodon pools during differentiation
a, Schematic of Pol III recruitment to tRNA genes. b, Representative ChIP–Seq signal at predicted tRNA genes in a locus on human chromosome 6 for RPC1 and BRF1. Data are from one biological replicate of hiPSC normalized to the estimated library sizes from counts over extended tRNA features (±125 bp) and scaled to reads per million (RPM). Insets: magnified views of regions around closely spaced tRNA loci. c, Correlation between tRNA abundance estimated by mim-tRNAseq (n = 373 unique transcripts) and RPC1 ChIP–Seq signal aligned to extended tRNA features (±125 bp) for hiPSC and neurons (mean from n = 2 biological replicates for each cell type; scaled to the proportions of total tRNA-mapped reads in each dataset). Solid blue lines, linear regression model; grey shading, 95% confidence interval; the Pearson’s correlation coefficients are indicated. d, Heatmaps of normalized RPC1 ChIP–Seq signal around tRNA gene start sites (±1 kbp) for single replicates. The tRNA genes were separated into housekeeping, repressed and inactive based on significant peaks in RPC1 ChIP–Seq data (FDR-adjusted P ≤ 0.05). e, UpSet plot of significant consensus RPC1 peaks (±125 bp) of annotated tRNA genes (FDR-adjusted P ≤ 0.05). Housekeeping tRNAs are shown in green and hiPSC-specific tRNAs in blue; the numbers in each group are indicated. f, Spike-in-normalized RPC1 ChIP–Seq read counts over tRNA features (±125 bp) versus the log2-transformed fold change in CM (left), NPC (middle) and neurons (right) relative to hiPSC presented as MA plots (n = 2 biological replicates for each cell type). Green and purple denote significantly higher and lower occupancies, respectively (FDR-adjusted P ≤ 0.05). Source numerical data are provided.
