Fig. 3: Khsrp depletion induces intron retention.

A Schematic diagram of the experimental setup. Mice (n = 2) were first infected with either AAV-shKhsrp or PX552 (control) for 2 weeks via tail-vein injection. Primary hepatocytes were then isolated and sorted using flow cytometry. Cells were divided into four groups, namely, PX552 GFP⁻ (Ctrl1), PX552 GFP⁺ (Ctrl2), shKhsrp GFP⁻ (Ctrl3), and shKhsrp GFP⁺ (shKhsrp), and prepared for RNA-Seq analysis. B, C Genome browser tracks of RNA-Seq signals at (B) Khsrp and at (C) Egfr and Sf3b1 in the Ctrl1, Ctrl2, Ctrl3, and shKhsrp groups. Tracks of RNA-Seq signals at the intron-retained regions are shown by dotted boxes. D Scatter plots show changes in splicing events between Ctrl3 and shKhsrp groups. Using rMATS, five types of AS events were analyzed: Retained introns (RIs), skipped exons, alternative 5′ and 3′ splice sites (A5SS and A3SS, respectively), and mutually exclusive exons. Significantly changed events (|ΔPSI| > 0.05, FDR < 0.05, and supporting reads ≥ 5) are shown by color dots. E Volcano plots showing up- or downregulated exons or introns in Ctrl3 or shKhsrp groups according to RNA-Seq analysis. F GO analysis based on RNA-Seq results showing mRNA expression from intron-retained genes after Khsrp-knockdown in primary hepatocytes (left). Heatmaps of mRNA splicing factors and cell cycle-related genes are also shown (right).