Study of the role of circPVT1 circRNA knockdown in cardiomyocytes

circPVT1, a circRNA derived from the circularization of the second exon of the long-non coding RNA PVT1, was found upregulated in ischemic heart failure patients. We performed RNA-Seq to assess the molecular changes that occurr upon circPVT1 knockdown in AC16 cells, a human cardiomyocyte cell line. Transcriptome analysis identified differentially expressed genes mainly involved in extracellular matrix formation, fibrosis and cellular senescence, suggesting the involvement of circPVT1 in cardiac remodeling. We used siRNAs to knockdown the expression of circPVT1 or linear PVT1 in AC16 cells. A non-targeting siRNA was used as a control. Each condition was done in quadruplicate and samples were collected 72h after siRNA transfection. We analyzed the differential expressed genes in circPVT1 knockdown cells in comparison to cells transfected with non-targeting siRNA control (FDR < 0.01) and in circPVT1 knockdown cells in comparison with linear PVT1 knockdown samples (FDR < 0.01). To identify genes specifically modulated by circPVT1 knockdown, we compared these two differential expression analyses and only overlapping genes were taken into account.