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Series GSE162627 Query DataSets for GSE162627
Status Public on Dec 07, 2020
Title Merkel Cell Polyomavirus Encodes Circular RNAs (circRNAs) Enabling a Dynamic circRNA/microRNA/mRNA Regulatory Network
Organisms Homo sapiens; Rattus norvegicus
Experiment type Other
Summary 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
Contributor(s) Abere B, Chang Y
Citation(s) 33323517
Submission date Dec 03, 2020
Last update date Jan 11, 2021
Contact name Bizunesh Abere
Phone 4126237733
Organization name Hillman Cancer Center
Department Cancer Virology Program
Lab Chang and Moore
Street address 5117 Centre Ave, Research Pav. Suite 1.8
City Pittsburgh
State/province PENNSYLVANIA
ZIP/Postal code 15213
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL22396 Illumina HiSeq 4000 (Rattus norvegicus)
Samples (4)
GSM4955658 CVG-1
GSM4955659 MS-1
GSM4955660 HEK-293 MCV-HF
BioProject PRJNA682427
SRA SRP295705

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Supplementary file Size Download File type/resource
GSE162627_RAW.tar 10.0 Kb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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