Fig. 4: UTP15 binds to chromatin activates pluripotency gene transcription.

a Average density profiles of sense and antisense CLIP read at the transcription start sites (TSSs) of protein-coding genes (n = 22,470). b Distribution of UTP15 ChIP-seq binding sites. c Average reads density (top) and heatmap (bottom) analysis of UTP15 CLIP-seq peaks around the center of UTP15 ChIP peaks (left panel). Average reads density (top) and heatmap (bottom) analysis of UTP15 ChIP-seq peaks around the center of UTP15 CLIP peaks (right panel). d Box plots represent UTP15 ChIP-seq signal intensity (log₂) at promoter regions of UTP15 ChIP target genes (n = 7,091 genes) after two hours of treatment with ActD (replicate 1). Box plots show the median (centre line), 25th–75th percentiles (box bounds), and whiskers extending to 1.5 × IQR; data points beyond the whiskers are considered outliers (not shown). Two-sided Mann-Whitney U test (left). Average density profiles of UTP15 ChIP-seq density at the TSSs of UTP15 ChIP target genes after ActD treatment (right). e Volcano plot showing the distribution of proteins captured by UTP15 Co-IP. IgG was used as a control. (p value < 0.05, fold change > 1.5). f Dual-luciferase reporter assay in 293T cells. GAL4 DNA-binding domain was fused to UTP15; 5 × upstream activation sequence (UAS) was added upstream of SV40 promoter. GAL4 DNA-binding domain alone was used as control. (mean ± SD, n = 3 biological replicates, two-sided Student’s t-test, **** p < 0.0001). GSEA analysis of embryonic genes (g) and ESC-high genes (h) in nascent RNA-seq after acute UTP15 degradation (4 h versus 0 h). i Nascent RNA qPCR analysis of pluripotency genes after acute UTP15 degradation. Relative gene level was normalized with spike-in RNA. (mean ± SD, n = 3 biological replicates, two-sided Student’s t-test, * p < 0.05, ** p < 0.01). j Nascent RNA qPCR analysis of pluripotency genes and 5’-ETS upon reintroduction of full-length UTP15 and NoLS mutant during acute UTP15 depletion. Relative RNA level was normalized to spike-in RNA (fold change of IAA 4 h versus 0 h). (mean ± SD, n = 4 biological replicates, two-sided Student’s t-test, ** p = 0.0093). k Nascent RNA qPCR analysis of pluripotency genes and 5’-ETS after acute POLR1A degradation. (mean ± SD, n = 4 biological replicates, two-sided Student’s t-test, * p = 0.0171). l Box plots represent POLR1A-AID PRO-seq signals for 685 UTP15 target genes following POLR1A degradation (n = 685 genes, box plots show the median (centre line), 25th–75th percentiles (box bounds), and whiskers extending to 1.5 × IQR, two biological replicates). Source data for Fig. 4f, i, j and k are provided as a Source Data file.