Exon-Resolved Dissection of Shared, Unique, and Antagonistic Functions of ZFAS1 Isoforms

The long noncoding RNA ZFAS1 plays a role in cell proliferation and has been linked to cancer development and prognosis. However, the ZFAS1 locus is predicted to encode over 40 ZFAS1 splice variants, which remain largely uncharacterized. To shed light on the role of ZFAS1 in hepatocyte models, we examined the transcriptome-wide effects of separately targeting three exons present in representative ZFAS1 variants with gapmer antisense oligonucleotides. Evidence of cross-exon compensatory regulation was obtained by qRT-PCR. Although targeting resulted in a subset of concerted transcript perturbations-indicating specificity and shared functionalities-the overall effects were predominantly non-redundant. Overrepresentation analyses revealed that proximal exon and distal exon targeting affected cell cycle and transcription regulation, respectively. Strikingly, interrogation of the entire transcriptome with gene set enrichment analysis identified a shared subset of pathways related to cell-cycle control and translation, which were affected antagonistically in an exon-dependent manner. Whereas targeting the proximal exon was predicted to broadly compromise cell-cycle and translational functions, targeting distal exons produced contrasting effects on these processes. Together, these findings demonstrate that the arrangement of ZFAS1 exons can markedly modulate its function.