Transfer RNA pools in human cells are controlled by selective gene expression [ATAC-seq]

Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. We find that tRNA transcript pools vary substantially, while the abundance of tRNAs with distinct anticodons, which governs decoding rates, is more stable among cell types. Mechanistically, RNA Polymerase III (Pol III) samples a wide range of tRNA genes in hiPSC and becomes constrained to a housekeeping subset upon differentiation. This is mediated by diminished mTOR signaling, which activates the Pol III repressor MAF1. Our data rationalize how tRNA anticodon pools are buffered in different cellular contexts and reveal that mTOR activity drives selective tRNA expression. Overall design: Human induce pluoripotent stem cells (hiPSC), and derived neural progenitors (NPC), mature neurons, and cardiomyocytes (CM) were cultured. Subsequent chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA Polymerase III subunit RPC1, TFIIIB subunit BRF1, histone modifications H3K4me3 and K3K27me3, ATAC-Seq, RNA-Seq, ribosome profiling followed by sequencing (Ribo-Seq) and tRNA-Seq datasets were generated to investigate the regulation of tRNA genes upon differentiation of hiPSCs.