Figure 5

PRL3 Restrains Pol II Transcriptional Elongation of DDX21 Target Genes at MITF Targets

(A) Venn diagram of overlapping genes between DDX21 ChIP targets (purple) and PRL3 5′-enriched genes (blue) (p = 7.63 e-99, Fisher's exact test). GO enrichment analysis of cellular components (false discovery rate [FDR] < 0.05). See also Table S4.

(B) DDX21 ChIP-seq data as log₂ ratios of PRL3 over-expressing (PRL3) versus empty vector (EV) control for all long (All genes) and 5'-enriched genes., ^∗∗p = 1.61 × 10⁻⁸, Wilcoxon signed-rank test.

(C) DDX21 ChIP-seq read profile for all long or 5′-enriched genes in control EV and PRL3-expressing cells. In 5′-enriched genes, PRL3 causes a net accumulation of DDX21 to the 5′ end (red arrows) versus EV control-treated cells (black arrow).

(D) Boxplots of RNAP II (total, Ser2P, and Ser5P) ChIP-seq data shown as ratios of PRL3 versus control read depth for all long genes and 5′-enriched genes. (5′-enriched p = 0.83, 1.26 × 10⁻¹⁸ 3.93 × 10⁻¹¹ for total, Ser2P, and Ser5P RNAP, respectively; Wilcoxon signed-rank test).

(E) RNAP II (Ser2P) ChIP-seq profile for 5′-enriched genes in EV control and PRL3-expressing cells. RNAP II (Ser2P) signal is decreased at the 5′ end (red arrow) and throughout the gene body versus control cells (black).

(F) 4sU RNA-seq and RNA PolII (Ser2P) ChIP-seq transcript coverage for ATP5F1A, an example 5′-enriched gene. In EV cells (gray) 4sU transcripts align with exons (gray arrows). In PRL3-expressing cells (red) transcripts are enriched at the 5′ end (red arrows) and RNAP II (Ser2P) depleted over the gene body versus EV control cells.

(G) MITF ChIP-seq signal surrounding the TSS (±1 kb) for non-5′-enriched (gray) and 5′-enriched (red) genes (p values determined using paired and un-paired Wilcoxon rank sum tests for within and between gene set comparisons, respectively).

(H) MITF ChIP-seq profile of ATP5V0D1, a 5′-enriched PRL3 target gene. Elevated MITF occupancy in PRL3 versus control EV cells proximal to the TSS.

(I) Venn diagram of DDX21 ChIP targets (white, 6,566 total), PRL3 5′-accumulated genes (pink, 1,745 total), and MITF ChIP targets (blue, 2,908 total). 162 genes overlap the three groups, highlighted in yellow (p = 6.67e−06, hypergeometric test). Table lists cellular component GO enrichment analysis of these 162 genes (FDR < 0.05). See also Table S4.