The overall goals of this project are to understand how polyoma virus RNAs are made and regulated in infected cells and to use this virus as a model system to learn more general rules for mammalian RNA processing and function. We have discovered that much regulation of viral gene expression depends on the formation of double-stranded RNAs and their editing by the cellular dsRNA specific adenosine deaminase (ADAR1). Experiments completed during the previous funding period suggested that the long-sought trigger for the viral early-late switch might be the overlap and perhaps also the editing of the early and late polyadenylation signals. This represents a new mechanism of gene regulation. We also learned much new about nuclear responses to dsRNAs, including the involvement of a long nuclear-retained noncoding RNA (NEAT1) in the assembly of nuclear bodies called paraspeckles, which function in the retention of edited RNAs. We will extend these studies in three related aims. In the first, we will use new methods to better characterize RNA expression in the viral life cycle and will determine the nature and interplay of DNA sequence elements that promote regulated gene expression. In the second aim we will examine more closely the fate of polyoma dsRNAs in the nucleus, and the impact of cellular dsRNA response pathways including paraspeckles on infection. In the final aim we will carry out studies to learn more about how antisense RNA works in mammalian nuclei. This work will involve studying whether single DNA molecules can allow concurrent transcription in both directions as well as a new approach using small molecule-directed heterodimerization to alter the intranuclear proximity of DNA and RNA molecules.

Public Health Relevance

Mouse polyoma virus regulates the expression of its genes in an unusual manner, involving the generation of double-stranded RNA (dsRNA) molecules which play an important role in the viral life cycle. This proposal is to learn more about the underlying mechanisms of gene regulation in this system and to apply these lessons to achieve a fuller understanding of the function and fate of dsRNAs in mammalian cells.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Virology - A Study Section (VIRA)
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Read-Connole, Elizabeth Lee
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University of Connecticut
Schools of Medicine
United States
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Carmichael, Gordon G (2016) Gene Regulation and Quality Control in Murine Polyomavirus Infection. Viruses 8:
Garren, Seth B; Kondaveeti, Yuvabharath; Duff, Michael O et al. (2015) Global Analysis of Mouse Polyomavirus Infection Reveals Dynamic Regulation of Viral and Host Gene Expression and Promiscuous Viral RNA Editing. PLoS Pathog 11:e1005166
Yang, Li; Duff, Michael O; Graveley, Brenton R et al. (2011) Genomewide characterization of non-polyadenylated RNAs. Genome Biol 12:R16
Chen, Ling-Ling; Carmichael, Gordon G (2010) Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol 22:357-64
Chen, Ling-Ling; Carmichael, Gordon G (2009) Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell 35:467-78
Gu, Rui; Zhang, Zuo; DeCerbo, Joshua N et al. (2009) Gene regulation by sense-antisense overlap of polyadenylation signals. RNA 15:1154-63
Gu, R; Zhang, Z; Carmichael, G G (2006) How a small DNA virus uses dsRNA but not RNAi to regulate its life cycle. Cold Spring Harb Symp Quant Biol 71:293-9
Wang, Qiaoqiao; Zhang, Zuo; Blackwell, Katherine et al. (2005) Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. Curr Biol 15:384-91
Wang, Qiaoqiao; Carmichael, Gordon G (2004) Effects of length and location on the cellular response to double-stranded RNA. Microbiol Mol Biol Rev 68:432-52
Huang, Y; Wimler, K M; Carmichael, G G (1999) Intronless mRNA transport elements may affect multiple steps of pre-mRNA processing. EMBO J 18:1642-52

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