GSE162627
Merkel Cell Polyomavirus Encodes Circular RNAs (circRNAs) Enabling a Dynamic circRNA/microRNA/mRNA Regulatory Network
Viral noncoding RNAs have acquired increasing prominence as important  regulators of infection and mediators of pathogenesis. Circular RNAs (circRNAs) generated  by backsplicing events have been identified in several oncogenic human DNA  viruses. Here, we show that Merkel cell polyomavirus (MCV), the etiologic cause of ~80%  of Merkel cell carcinomas (MCCs), also expresses circular RNAs. By RNase R-resistant RNA  sequencing, four putative circRNA backsplice junctions (BSJs) were identified from the  MCV early region (ER). The most abundantly expressed MCV circRNA, designated circMCVT,  is generated through backsplicing of all of ER exon II to form a 762-nucleotide (nt) circular  RNA molecule. Curiously, circMCV-T, as well as two other less abundantly expressed  putative MCV circRNAs, overlaps in a complementary fashion the MCV microRNA (miRNA)  locus that encodes MCV-miR-M1. circMCV-T is consistently detected in concert with linear  T antigen transcripts throughout infection, suggesting a crucial role for this RNA molecule  in the regulatory functions of the early region, known to be vital for viral replication.  Knocking out the hairpin structure of MCV-miR-M1 in genomic early region expression  constructs and using a new high-efficiency, recombinase-mediated, recircularized  MCV molecular clone demonstrates that circMCV-T levels decrease in the presence of  MCV-miR-M1, underscoring the interplay between MCV circRNA and miRNA. Furthermore,  circMCV-T partially reverses the known inhibitory effect of MCV-miR-M1 on early gene  expression. RNase R-resistant RNA sequencing of lytic rat polyomavirus 2 (RatPyV2) identified  an analogously located circRNA, stipulating a crucial, conserved regulatory function of  this class of RNA molecules in the family of polyomaviruses. Overall design: Ribodepleted RNaseR treated total RNA from MCV positive MCC derived cell lines, RatPyV2 positve rat parotid tissue or 293 cell transfected with a recircularized MCV-HF genome was used for RNA sequencing