PVT1 splicing activity predicts genome-wide gene expression with miRNA regulatory signatures

Abstract

Long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression, yet the functional impact of their splicing activity remains poorly understood. Here, we focus on the chromatin-associated lncRNA PVT1, whose splicing efficiency at specific 3 splice sites predicts expression of distal genes in breast cancer. Using elastic net modeling across hundreds of breast cancer samples, we identify PVT1 splicing activity as a predictor of gene expression signatures enriched in miR-200/205 targets. Causal inference analysis using tumor-specific SNVs confirms that perturbation of splicing at specific sites alters the expression of distal gene sets enriched in miR-200/205 targets. We suggest a mechanistic model in which inefficient splicing and intron retention expose intronic miR-200 seed sites, perfect 7-mers, found exclusively within PVT1 introns, enabling PVT1 to function as a chromatin-associated lncRNA with intron-retained competing endogenous (ceRNA) activity. Artificial splicing enhancement of PVT1 in vitro with CASFx altered the expression of miR-200 target genes supporting this model. A genome-wide screen for intronic miR-200 seed sites, and splicing-based modeling across additional lncRNAs and protein-coding genes, identified PVT1 as a top candidate for splicing-modulated intron-retained ceRNA activity. Cross-tissue model generalization to prostate cancer supports the broader relevance of PVT1 splicing-based regulation. Our results highlight the regulatory potential of lncRNA splicing activity in trans, suggesting that chromatin-tethered, intron-retained lncRNAs such as PVT1 may serve as key post-transcriptional regulators in cancer.