Fig. 5: Usp39 deletion leads to altered splicing of autophagy-related genes in hepatocytes. | Nature Communications

Fig. 5: Usp39 deletion leads to altered splicing of autophagy-related genes in hepatocytes.

From: Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy

Fig. 5

a Pie chart showing the distribution of AS events in the RNA-seq data in the livers of 5-week-old control and Usp39-HKO male mice (n = 4 per group) fasted 16 h. A total of 1937 splicing events from 1472 genes were identified. SE, skipped exons; RI, retained introns; A5SS, alternative 5’ splice site; A3SS, alternative 3’ splice site; MXE, mutually exclusive exons (p < 0.05, |delInclevel| > 0.1). b Heatmap of autophagy-related genes using RNA-seq data of control and Usp39-HKO male mice (n = 4 per group). c Volcano plot showing differential AS events in the RNA-seq data of livers from Usp39-HKO male mice compared to controls. Negative log10 transformed p-values and the delInclevel values were analyzed with rMATS (n = 4 per group). d The distribution of Usp39 binding peaks (35, 980), corresponding to 5002 genes, were identified from RIP-seq data with Piranha software (-p 0.001 -z 100). e HOMER de novo motif analysis of Usp39 binding peaks based on the RIP-seq data showing top-two Usp39 binding motifs. Binding motifs were ranked by p-value, and the statistical results including the percentage of targets and, the background are shown. f Venn diagram of 611 overlap genes from 5002 Usp39 binding genes (RIP-seq) and 1472 differentially expressed genes (RNA-seq). g Biological process enrichment analysis of the 611 genes from (f). Accumulative hypergeometric q-values and gene ratios were calculated. h–k Sashimi plots of AS and binding peaks for indicated genes using RNA-seq and RIP-seq data. The light blue region highlights the AS sites and the Usp39 binding region. l PCR was performed to analyze AS events in indicated genes using splice-variant specific primers in the liver tissues of 5-week-old control and Usp39-HKO male mice. Images are representative of at least three independent experiments. The results are presented as the mean ± S.D. NS, stands for non-significant. RIP, RNA immunoprecipitation sequencing. AS, alternative splicing. Source data are provided as a Source data file.

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