Fig. 5: Identification of YTHDC1 binding targets in urothelial cells via RIP-seq.

a Representative Western blot showing YTHDC1 protein abundance in DMSO- and STM2457-treated wild-type UROtsa cells. IgG was used as an IP control. b Read counts (upper panel) from YTHDC1 RIP-seq data in the DMSO group, demonstrating enriched YTHDC1 binding across all transcripts. Blue line: YTHDC1 pulldown; red line: input signal. Heatmap (lower panel) showing enrichment of YTHDC1-bound transcripts in the 5’ to 3’ direction. Each row corresponds to a transcript bound by YTHDC1, where the intensity of the color reflects the enrichment level, with the scale bar shown on the right. c Pie charts displaying the distribution of YTHDC1 RIP-seq peaks in the DMSO and STM2457 groups (q < 0.01). d Venn diagram indicating the number of YTHDC1 binding targets in the DMSO and STM2457 treatment groups. p-value < 0.05. e Representative genome tracks depicting an example gene, STEAP1, bound by YTHDC1, with lower peaks in the STM2457 treatment group than in the DMSO group. f Heatmaps illustrating enriched YTHDC1 binding (normalized against the input control) in the DMSO and STM2457 treatment groups for all high-confidence YTHDC1-bound transcripts (determined by Diffbind, log₂fold change < −1, p-value < 0.05). g Upper row: enriched motifs in YTHDC1-bound sequences identified by RIP-seq in the DMSO group (p-value = 1e-35); lower row: enriched motifs in YTHDC1-bound sequences identified by RIP-seq in the high-confidence group (p-value = 1e-22). h Venn diagram showing the intersection among high-confidence YTHDC1-bound transcripts, m⁶A-modified transcripts, and differentially expressed transcripts in YTHDC1-depleted cells ( | log₂fold change | > 1.5, q-value < 0.05). The intersecting genes are listed in the middle, and representative peaks (signal intensity) are shown in the right panel to demonstrate the overlap between m⁶A peaks (GLORI⁵²) and YTHDC1 binding peaks (RIP-seq).