Fig. 3

Dynamic domain-level regulation of tRNA gene transcription during macrophage differentiation. a Visualization of chromatin and transcriptional dynamics at an example tDNA locus on chromosome 5. Top: in situ Hi-C contact frequency matrix in THP-1 monocytes. *Asterisk represents long-range loop anchor region presented in Fig. 4c. Middle: mean log2(fold change) signal tracks for chromatin accessibility (ATAC-seq; blue), H3K27 acetylation (ChIP-seq; green), RNA polymerase III occupancy (ChIP-seq; orange), and nascent RNA (Biotin-capture RNA-seq; red) across two adjacent contact domains and neighboring tDNA clusters. Bottom: gene structure and physical contact domain border locations. log2(fold change) represents ± 72 h PMA treatment. Gene structure includes both tRNA genes and proximal RNAPII-transcribed genes. Lower panel depicts corresponding contact domain borders in THP-1 monocytes. b Mean log2(fold change) in normalized signal track read density for ATAC-seq, H3K27ac, POLR3D, and Biotin-capture RNA-seq across all human tRNA genes ± 1 Kb (−1000 upstream, +1000 downstream). c Mean log2(fold change) of integrated tDNA expression values across individual tRNA genes and mean log2(integrated tDNA expression) comparing THP-1 cells ± 72 h PMA treatment. Triangles represent individual tRNA genes that are upregulated (red) and downregulated (blue) at an FDR threshold of 0.15, including significant nmt-tDNAs (gold). d Arrow plot representation of aggregate nascent tRNA dynamics collapsed by tRNA-type vs. codon usage frequency (labeled by anticodon). Arrow-head represents log2(tDNA expression) and cognate codon usage after 72 h PMA treatment; arrow-bottom represents log2(tDNA expression) and cognate codon usage in untreated THP-1 monocytes. e log2(fold change) in closest RNAPII-transcribed genes for downregulated (blue), upregulated (red), and non-differential (n.d., gray) tRNA genes (top **p = 1.58^-5; bottom *p = 0.047, Wilcoxon rank-sum test). f Median cluster-wide log2(fold change) for tDNA clusters harboring downregulated (blue), upregulated (red), and non-differential (gray) tRNA genes (top **p = 0.0056, bottom **p = 6.41^-6, Wilcoxon rank-sum test). g Median contact domain-wide log2(fold change) for tDNA clusters harboring downregulated (blue), upregulated (red), and non-differential (gray) tRNA genes (top *p = 0.016; bottom **p = 0.0022, Wilcoxon rank-sum test)