ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/020/SRR32946820/SRR32946820.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/028/SRR32946828/SRR32946828.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/034/SRR32946834/SRR32946834.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/031/SRR32946831/SRR32946831.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/022/SRR32946822/SRR32946822.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/026/SRR32946826/SRR32946826.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/024/SRR32946824/SRR32946824.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/035/SRR32946835/SRR32946835.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/030/SRR32946830/SRR32946830.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/027/SRR32946827/SRR32946827.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/021/SRR32946821/SRR32946821.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/018/SRR32946818/SRR32946818.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/033/SRR32946833/SRR32946833.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/032/SRR32946832/SRR32946832.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/029/SRR32946829/SRR32946829.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/019/SRR32946819/SRR32946819.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/023/SRR32946823/SRR32946823.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR329/025/SRR32946825/SRR32946825.fastq.gzprimaryOK200GenomicsUniversity of Illinois Urbana-Champaignhttps://www.ebi.ac.uk/ena/browser/view/PRJNA1245165Homo sapiensRNA polymerase III (Pol III) transcription in cancer is linked with the emergence of snaR-A (small NF90-associated RNA isoform A), a hominid-specific ncRNA shown to enhance cell proliferation, migration, and invasion. Here, we investigate snaR-A-protein interactions to delineate its role as a putative driver of cancer progression. At the molecular level, we discover that snaR-A interacts with mRNA splicing factors, including SF3B2 - a core component of the U2 small nuclear ribonucleoprotein (snRNP) - and localizes to subnuclear foci enriched for splicing factors. Ectopic snaR-A overexpression leads to increased intron retention, a hallmark of inefficient splicing, whereas depletion of endogenous snaR-A reduces intron retention in mRNA subpopulations associated with 3’ intron-exon U2 snRNP residency and nuclear speckle proximity. We further show that high levels of snaR-A promotes cell migration in cells linked with increased intron retention, consistent with evidence supporting snaR-A as a negative prognostic factor in cancer. Taken together, these findings establish snaR-A as a molecular disruptor of splicing. We propose that snaR-A-related splicing disruption may phenocopy previously reported splicing defects and consequences attributed to mutations in U2 snRNP in cancer, eliciting an alternate, non-mutational pathway during tumorigenesis. Overall design: To investigate the effect of SSB on snaR-A, we performed SSB knockdown in HEK293T and sequenced the samples. The experiment included three biological replicates for scramble and SSB knockdown. Raw mRNA signal counts were extracted.ENAfalseCancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulationsCancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations2025-09-242025-05-01PRJNA1245165GSE2935489606