Differential regulation of ZFAS1 splice variants by endoplasmic reticulum stress in hepatocyte cell lines

The suppression of the long noncoding RNA (lncRNA) TRIBAL in hepatocytes was recently shown to affect the expression of pivotal regulators and hundreds of poorly understood or uncharacterized transcripts. The most upregulated transcript corresponded to a predicted splice variant of the lncRNA ZFAS1. Here, we characterize and investigate the role and regulation of ZFAS1 splice variants in liver cell models. New ZFAS1 splice variants were identified, all of which were enriched in the cytoplasm of HepG2 cells. TRIBAL suppression strongly upregulated a low-abundance ZFAS1 variant in hepatocytes but not in hepatoma models. However, preventing the upregulation of the ZFAS1 splice variant did not mitigate the impact of TRIBAL suppression in hepatocytes. ZFAS1 variants were rapidly but differentially increased in response to thapsigargin, which causes endoplasmic reticulum (ER) stress and activates the unfolded protein response (UPR). Inhibition of PERK, a central sensor of the UPR, had contrasting impacts on ZFAS1 variants in response to thapsigargin. Moreover, whereas the upregulation of the main ZFAS1 form was reduced by the suppression of the UPR mediators ATF4 and NFE2L2 (also known as NRF2), the other variants were not. Lastly, ZFAS1 suppression decreased cell viability both at baseline and in response to acute thapsigargin treatment. This work identifies novel ZFAS1 variants and uncovers a link between ER stress and ZFAS1 through the UPR.