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Fig. 5 | Genome Biology

Fig. 5

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

Fig. 5

Differential transcription of tRNA genes coincides with enhanced MAF1 occupancy and dynamic TF binding. a Comparison of log2(expression) levels for TFs in THP-1 monocytes (x-axis) and THP-1 macrophages (y-axis). Triangles represent relevant genes encoding RNAPIII transcription machinery (black), MAF1 (purple), ARNT (orange), HIF1A (yellow), HINFP (blue), and EGR1 (red). Triangles do not denote statistical significance. b Mean read density of MAF1 ChIP-seq (RPGC mean normalized read per genomic content) at all tRNA genes in THP-1 cells before (gray) and after treatment with PMA (purple). c Mean log2(fold change) of MAF1 ChIP-seq read density at all downregulated (blue), upregulated (red), and non-differential (gray, n.d.) tRNA genes. d log2(fold change) of the closest MAF1 ChIP-seq peak for all downregulated (blue), upregulated (red), and non-differential (gray) tRNA genes (*p = 0.024, n.s. not statistically significant; Wilcoxon rank-sum test). e Enrichment of TF footprints identified by PIQ [75] within tDNA domains (x-axis) and clusters (y-axis). Enrichment measured as log10(observed/expected). Inset: illustration of ATAC-seq based footprinting analysis. Read ends represent hyperaccessible DNA adjacent to protected TF binding sites. f Comparison of dynamic H3K27ac levels at all footprints identified by PIQ. Differential accessibility scores were binned by the number of standard deviations from the average differential score across more than 2 million footprints (Additional file 1: Figure S6b). (+) denotes increased accessibility score, (−) denotes decreased accessibility score. Colored overlay represents strong differential accessibility score (≥2 standard deviations from the mean differential score) in THP-1-derived macrophages. g Comparison of dynamic ARNT::HIF1A footprint accessibility with the change in integrated tDNA expression at the nearest tDNA. h Comparison of dynamic HINFP footprint accessibility with the change in integrated tDNA expression at the nearest tDNA. i Comparison of dynamic EGR1 footprint accessibility with the change in integrated tDNA expression at the nearest tDNA

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