Fig. 3: snaR-A expression is associated with higher levels of intron retention (IR), consistent with perturbations of mRNA splicing efficiency. | Nature Communications

Fig. 3: snaR-A expression is associated with higher levels of intron retention (IR), consistent with perturbations of mRNA splicing efficiency.

From: Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations

Fig. 3: snaR-A expression is associated with higher levels of intron retention (IR), consistent with perturbations of mRNA splicing efficiency.

a RT-qPCR analysis of snaR-A RNA and 5S rRNA levels in HEK293T or A549 cells transfected with snaR-A (red) or scramble RNA (black) overexpression constructs. (n = 3 biological replicates). b Immunoblot analysis of SF3B2 and eGFP protein abundance in HEK293T or A549 cells transfected with flag-tagged SF3B2 (blue) or flag- tagged eGFP (green) overexpression constructs (n = 3 biological replicates). c Overview of transcript-level intron retention (IR) analysis. IRFinder intron ratios are compared between experiment (red) and control treatments (gray). Delta IR values computed as standardized log2(fold change) are summarized for (n) intron events and compared against a randomization-based null distribution of (n) introns. d, e Distributions of transcript-level delta IR z-scores in HEK293T or A549 cells following snaR-A (d) or SF3B2 overexpression (e). f Illustrative overview of siRNAs and related target regions tested against snaR-A. g RT-qPCR analysis of snaR-A knockdown results using siRNAs illustrated in panel f. siRNA #1, #2, and #3 successfully reduced snaR-A levels by >= 50%. h Distribution of transcript-level delta IR z-scores in HEK293T cells following snaR-A depletion using siRNA #1, #2, or #3. Source data are provided as a Source Data file.

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