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Fig. 1 | Genome Biology

Fig. 1

From: Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation

Fig. 1

Integrated tDNA expression and chromatin profiling in THP-1 monocytes. a Correlation between tRNA gene expression as measured by biotin-capture of nascent, demethylated tRNAs and by RNA polymerase III occupancy mapping by ChIP-seq (black; Spearman’s rank correlation coefficient = 0.74; p < 10^-16). Integrated tDNA expression profile (red) utilizes the mean normalized count for each tRNA gene. b Example signal track representation of the chromatin accessibility (ATAC-seq, blue), active histone signature H3K27 acetylation (ChIP-seq, green), RNA polymerase III occupancy (ChIP-seq, orange), and nascently transcribed RNA (Biotin-capture, red) at a tDNA cluster located on chromosome 6. RPGC mean normalized reads per genomic content. c Correlation between integrated tDNA expression profile with H3K27ac ChIP-seq levels surrounding tRNA genes (black; Spearman’s rank correlation coefficient = 0.55; p < 10^-16) and with chromatin accessibility at tRNA genes as measured by ATAC-seq (blue; Spearman’s rank correlation coefficient = 0.79; p < 10^-16). d Number of tRNA genes, tDNA clusters, and physical contact domains containing tRNA genes in human THP-1 cells. e Median intra-cluster tDNA expression range (gray) and interquartile range (IQR; red) as a function of tDNA cluster size (number of tRNA genes present within each cluster). Dotted lines represent median range and IQR for randomly shuffled tRNA genes within tDNA clusters (100,000 permutations). f Median intra-domain tDNA expression range (gray) and IQR (blue) as a function of tDNA contact domain size (number of tRNA genes located within each contact domain). Dotted lines represent median range and IQR for randomly shuffled tRNA genes within contact domains (100,000 permutations). In the case of overlapping contact domains, tRNA genes were assigned to the single smallest resident domain. g Distribution of integrated tDNA expression values segregated by proximity to nearest RNA polymerase II-transcribed gene (>100 Kb; n = 81; 20–100 Kb; n = 232; < 20 Kb; n = 295; **p = 1.18^-10, *p = 0.02, Wilcoxon rank-sum test)

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