RNA-seq analysis in HEK293T WT and SCARNA15-KO cells

Small Cajal body-specific RNAs (scaRNA) are conserved small noncoding RNAs that guide post-transcriptional modification of spliceosomal RNA (snRNA), a key step for accurate spliceosome biogenesis and function. Despite scaRNA expression being altered in cancer, how this impacts pre-mRNA splicing remains mostly unexplored. Here, we uncovered SCARNA15 as a critical regulator of cancer-promoting alternative splicing (AS) and stress adaptation. Our scaRNA expression analysis reveals a remarkable SCARNA15 upregulation during malignant transformation, which ensures pseudouridylation (Y) within a functional region of the U2 snRNA. This fines tune AS of distinct transcripts encoding oncoproteins and tumor-suppressors including central p53 regulators. Critically, SCARNA15 loss leads to aberrant p53 hyperactivation and impaired cancer cell survival in response to oxidative stress. Accordingly, SCARNA15-mediated redox homeostasis impacts cancer cell survival, movement and anchorage-independent growth. In sum, these findings highlight a functional role for SCARNA15 and Y in directing cancer-promoting AS programs in human cells. Overall design: 3 sets of samples including HEK293T WT and HEK293T SCARNA15-KO clone1 were included in the study. Each sample was biologically independent, matched triplicates.