Fig. 2

Organization and transcription of multicopy tRNA genes in humans. a Circular visualization of human tRNA gene coordinates across human chromosomes. Track descriptions from outermost moving inward: (1) Individual chromosome ideograms and cytogenetic band positions. (2) Location of tRNA genes (blue) and nuclear-encoded mitochondrial nmt-tRNA genes (red). *Asterisk represents approximate location of variable number tandem repeat (VNTR) on chromosome 1. (3) tRNA genes labeled by tRNA anticodon family and colored by amino acid isoacceptor family (note: not all tDNAs are directly labeled due to size and legibility constraints). (4) Biotin-capture based assay measuring nascent demethylated tRNAs (red). (5) ChIP-seq experiments mapping RNA polymerase III occupancy on tRNA genes (orange). (6) ATAC-seq experiments measuring chromatin accessibility at tRNA genes (blue). (7) ChIP-seq experiments capturing H3K27 acetylation levels at tRNA genes (green). (8) Link-plot of DNA loops identified by in situ Hi-C experiments proximal to tRNA genes (gray). b Median estimated human tRNA gene count for each anticodon tRNA family, colored by amino acid, as determined using a read-depth approach over several deeply sequenced whole-genome datasets from the 1000 Genomes Project. *Asterisks represent tRNA-types located on VNTR that show significant variation across sampled individuals. c Correlation between integrated tDNA expression, collapsed by anticodon tRNA family, with multi-copy tRNA gene count (Spearman’s rank correlation coefficient = 0.55; p = 1.0e-04). d Correlation between integrated tDNA expression, collapsed by anticodon tRNA family, and the frequency of cognate codon usage in the THP-1 transcriptome for multicopy tRNA genes (Spearman’s rank correlation coefficient = 0.51; p = 1.9e-04)