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

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