Characterization of the polyomavirus late polyadenylation signal

Biology of Polyomavirus miRNA

Polyomaviruses are a family of non-enveloped DNA viruses with wide host ranges. Human polyomaviruses typically cause asymptomatic infection and establish persistence but can be reactivated under certain conditions and cause severe diseases. Most well studied polyomaviruses encode a viral miRNA that regulates viral replication and pathogenesis by targeting both viral early genes and host genes. In this review, we summarize the current knowledge of polyomavirus miRNAs involved in virus infection. We review in detail the regulation of polyomavirus miRNA expression, as well as the role polyomavirus miRNAs play in viral pathogenesis by controlling both host and viral gene expression. An overview of the potential application of polyomavirus miRNA as a marker for the progression of polyomaviruses associated diseases and polyomaviruses reactivation is also included.

Control of Archetype BK Polyomavirus MicroRNA Expression

BK polyomavirus (BKPyV) is a ubiquitous human pathogen, with over 80% of adults worldwide being persistently infected. BKPyV infection is usually asymptomatic in healthy people; however, it causes polyomavirus-associated nephropathy in renal transplant patients and hemorrhagic cystitis in bone marrow transplant patients. BKPyV has a circular, double-stranded DNA genome that is divided genetically into three parts: an early region, a late region, and a noncoding control region (NCCR). The NCCR contains the viral DNA replication origin and cis-acting elements regulating viral early and late gene expression. It was previously shown that a BKPyV microRNA (miRNA) expressed from the late strand regulates viral large-T-antigen expression and limits the replication capacity of archetype BKPyV. A major unanswered question in the field is how expression of the viral miRNA is regulated. Typically, miRNA is expressed from introns in cellular genes, but there is no intron readily apparent in BKPyV from which the miRNA could derive. Here, we provide evidence for primary RNA transcripts that circle the genome more than once and include the NCCR. We identified splice junctions resulting from splicing of primary transcripts circling the genome more than once, and Sanger sequencing of reverse transcription-PCR (RT-PCR) products indicates that there are viral transcripts that circle the genome up to four times. Our data suggest that the miRNA is expressed from an intron spliced out of these greater-than-genome-size primary transcripts.IMPORTANCE The BK polyomavirus (BKPyV) miRNA plays an important role in regulating viral large-T-antigen expression and limiting the replication of archetype BKPyV, suggesting that the miRNA regulates BKPyV persistence. However, how miRNA expression is regulated is poorly understood. Here, we present evidence that the miRNA is expressed from an intron that is generated by RNA polymerase II transcribing the circular viral genome more than once. We identified splice junctions that could be generated only from primary transcripts that contain tandemly repeated copies of the viral genome. The results indicate another way in which viruses optimize expression of their genes using limited coding capacity.

How a small DNA virus uses dsRNA but not RNAi to regulate its life cycle

Mouse polyomavirus contains a circular DNA genome, with early and late genes transcribed from opposite strands. At early times after infection, genes encoded from the early transcription unit are predominantly expressed. After the onset of viral DNA replication, expression of genes encoded from the late transcription unit increases dramatically. At late times, late primary transcripts are inefficiently polyadenylated, leading to the generation of multigenomic RNAs that are precursors to mature mRNAs. These transcripts contain sequences complementary to the early RNAs and downregulate early-strand gene expression by inducing RNA editing. Our recent work leads to a model where the production of the multigenomic late RNAs is also controlled by the editing of poly(A) signals, directed by overlapping primary transcripts.