Fig. 6
From: Identification of UBA7 expression downregulation in myelodysplastic neoplasm with SF3B1 mutations
UBA7 alternative splicing events and gene expression are dysregulated in SF3B1 mutant MDS cells. (A) Boxplot showing the Percent-Spliced-In (PSI) values for intron retention (IR) events in UBA7, comparing wild-type (WT, blue) and SF3B1-mutant (red) samples. A significant increase in IR is observed in SF3B1-mutant samples (****p < 0.0001). (B) Boxplot displaying the PSI values for alternative 3’ splice site (A3SS) events in UBA7, with SF3B1-mutant samples (red) exhibiting significantly higher PSI values compared to WT (blue) (****p < 0.0001). (****FDR < 0.0001, ***FDR < 0.001, **FDR < 0.01, *FDR < 0.05). (C) Sashimi plot comparing RNA-seq read coverage and splicing patterns for UBA7 between SF3B1-mutant (red) and WT (blue) samples, focusing on a specific genomic region. Numbers on the curved lines represent the average junction-spanning read counts across biological replicates, normalized using RPKM. The average number of junction-spanning reads is clearly higher in WT samples compared to SF3B1-mutant samples, indicating reduced splicing efficiency in the mutant group. (D) Sashimi plot comparing another genomic region of UBA7 between SF3B1-mutant (red) and WT (blue) samples, showing similar trends with higher junction-spanning read counts in WT samples. The bottom black tracks represent the genomic localization of splicing events, providing a structural overview of exon–intron junctions. This figure highlights the spliceosome-mediated dysregulation of UBA7 in SF3B1-mutant samples, characterized by increased intron retention, alternative 3’ splice site usage, and reduced splicing efficiency compared to wild-type samples.
