Increased local abundance and not isoform identity of Pvt1 lncRNA promotes Myc repression during stress

Many long noncoding RNA (lncRNA) loci give rise to multiple isoforms as a result of alternative transcription start sites (TSS), transcription termination sites, and splicing. Whether or not lncRNA isoforms harbor unique functional elements is not known. Previous work identified two distinct set of variants in the Pvt1 lncRNA locus - the constitutively expressed isoforms initiated from exon 1a (Pvt1a) and the p53-induced isoforms initiated from a downstream exon 1b (Pvt1b). Pvt1b was proposed to act in cis to repress the transcription of the neighboring Myc proto-oncogene during the p53-mediated response to genotoxic and oncogenic stress. To investigate whether Pvt1b harbors isoform-specific elements that mediate its cis-repressive function, we utilized a luciferase reporter assay for cis-repression as well as developed genetically engineered mice and cells with Pvt1b-specific inhibition. Our results revealed that Pvt1b contributes to but is not required for cis repression. In in vivo and in vitro models of genotoxic and oncogenic stress, we observed that upregulation of Pvt1a isoforms compensated for Pvt1b loss, resulting in Pvt1b deficiency having a moderate effect on overall Pvt1 abundance, Myc regulation, and cellular stress responses. Long-read sequencing in the absence and presence of p53 activation exposed an unexpected diversity of stress-induced Pvt1 isoforms, further arguing against Pvt1b-specific functions. We propose that stress-induced increase in overall Pvt1 abundance rather than isoform-specific functional elements mediate Myc repression during stress.