Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy

Tan, X., Lu, Z. J., Gao, G., Xu, Q., Hu, L., Fellmann, C., Li, M. Z., Qu, H., Lowe, S. W., Hannon, G. J., Elledge, S. J. (2012) Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy. Proceedings of the National Academy of Sciences of the United States of America, 109 (3). pp. 869-874. ISSN 00278424 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/22219365
DOI: 10.1073/pnas.1119873109

Abstract

shRNAs can trigger effective silencing of gene expression in mammalian cells, thereby providing powerful tools for genetic studies, as well as potential therapeutic strategies. Specific shRNAs can interfere with the replication of pathogenic viruses and are currently being tested as antiviral therapies in clinical trials. However, this effort is hindered by our inability to systematically and accurately identify potent shRNAs for viral genomes. Here we apply a recently developed highly parallel sensor assay to identify potent shRNAs for HIV, hepatitis C virus (HCV), and influenza. We observe known and previously unknown sequence features that dictate shRNAs efficiency. Validation using HIV and HCV cell culture models demonstrates very high potency of the top-scoring shRNAs. Comparing our data with the secondary structure of HIV shows that shRNA efficacy is strongly affected by the secondary structure at the target RNA site. Artificially introducing secondary structure to the target site markedly reduces shRNA silencing. In addition, we observe that HCV has distinct sequence features that bias HCV-targeting shRNAs toward lower efficacy. Our results facilitate further development of shRNA based antiviral therapies and improve our understanding and ability to predict efficient shRNAs.

Item Type: Paper
Uncontrolled Keywords: RNA secondary structure shRNA optimization antivirus agent genomic RNA short hairpin RNA antiviral activity antiviral therapy article CD4+ T lymphocyte controlled study drug efficacy drug potency drug targeting gene expression gene silencing HeLa cell Hepatitis C virus human human cell Human immunodeficiency virus Influenza virus nonhuman priority journal protein secondary structure RNA structure sensor virus DNA cell DNA interaction virus gene virus genome Antiviral Agents Base Sequence Cells, Cultured Genetic Testing Genome, Viral HeLa Cells Hepacivirus HIV Humans Influenza A virus Nucleic Acid Conformation Reproducibility of Results RNA Interference RNA, Small Interfering Viruses Mammalia
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > shRNA
organism description > virus
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL labs > Lowe lab
CSHL Cancer Center Program > Cancer Genetics
Depositing User: Matt Covey
Date: 2012
Date Deposited: 09 Jan 2013 16:12
Last Modified: 02 Jan 2018 20:06
PMCID: PMC3271875
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26413

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