SRA

Merkel cell polyomavirus (MCPyV) is considered the etiological agent of Merkel cell carcinoma and persists asymptomatically in the majority of its healthy hosts. Due to the lack of appropriate model systems, the mechanisms of viral replication and MCPyV persistence remain poorly understood. We have used a semi-permissive replication system to study expression and functions of the MCPyV-encoded miRNA mcv-miR-M1 during during short and long-term replication of authentic MCPyV episomes. RNA-seq analysis of small RNAs demonstrates that replicating MCPyV episomes express the viral miRNA is at very high levels, whereas Merkel carcinoma-derived cell lines (MCCL) produce only very little mcv-miR-M1. Our RNA-seq analysis of polyadenylated transcripts delineates the structures of early and late viral transcripts and suggests that most transcripts derived from the early region are subject to mcv-miR-M1-mediated cleavage. Additionally, ChIP-seq analyses demonstrates that LT-Ag binds to the viral origin of replication (but not to other regions of the viral episome), and furthermore reveals the existence of H3K4me3 enriched chromatin regions on the replication origin as well as a region immediately upstream of the genomic miRNA locus. The latter observation is consistent with the fact that the viral miRNA can be autonomously expressed from a subgenomic fragment of the early coding region.