SCAR-6 elncRNA locus epigenetically regulates PROZ and modulates coagulation and vascular function

Syntenic conservation is an effective strategy to identify evolutionarily conserved lncRNA orthologs. In this study, we identified a novel uncharacterized conserved lncRNA known as Syntenic Cardiovascular Conserved Region-Associated lncRNA-6 (scar-6) and functionally validated its role in coagulation and cardiovascular function. Precise editing of the scar-6 lncRNA locus in zebrafish (scar-6gib007Δ12/Δ12) resulted in cranial hemorrhage and permeability defects. Further analysis, including overexpression, locus editing, and rescue experiments, provided compelling evidence for the critical role of the scar-6 transcript in the coagulation process of zebrafish. Notably, rescue attempts were unsuccessful in mitigating cranial hemorrhage. Molecular investigation revealed that the scar-6 RNA acts as an enhancer lncRNA (elncRNA), and controls the expression of prozb, an inhibitor of factor Xa, through the enhancer element on its locus. The scar-6 locus actively suppresses the loop formation between prozb and scar-6 sequences, facilitated by methylation of CpG island via the prdm14-PRC2 complex, which is stabilized by the scar-6 elncRNA transcript. Disruption of this mechanism in scar-6gib007Δ12/Δ12 zebrafish led to impaired vascular function and subsequent hemorrhage. This was triggered by the activation of the PAR2 receptor mediated by upregulation of prozb, which in turn caused NF-κB-mediated endothelial cell activation. This study presents novel evidence for the multifaceted function of the scar-6 locus, highlighting its crucial role in regulating the coagulation cascade gene prozb and maintaining homeostasis and vascular function.