Unknown,Transcriptomics,Genomics,Proteomics

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Global gene expression profiling of mouse liver tissue samples after treated with various anti-HCV shRNAs


ABSTRACT: RNA interference (RNAi) is becoming routine in scientific discovery and treating human disease. However, its applications are hampered by unwanted effects. The RNA-Seq analyses from mouse liver samples expressing various anti-HCV shRNAs show that weak base-pairing in both seed and 3’ regions is required to achieve minimal off-targeting effect. We created nine shRNAs against the HCV genome, and transfected shRNA-expressing plasmids into mouse liver via a hydrodynamic tail vein infusion. A plasmid backbone lacking the shRNA sequence was used as a negative control. After 7 days, mouse liver RNAs were harvested and subject to RNA-Seq analysis (two biological repeats).

ORGANISM(S): Mus musculus

SUBMITTER: Yue Zhang 

PROVIDER: E-GEOD-55131 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.

Gu Shuo S   Zhang Yue Y   Jin Lan L   Huang Yong Y   Zhang Feijie F   Bassik Michael C MC   Kampmann Martin M   Kay Mark A MA  

Nucleic acids research 20140930 19


The use of RNA interference is becoming routine in scientific discovery and treatment of human disease. However, its applications are hampered by unwanted effects, particularly off-targeting through miRNA-like pathways. Recent studies suggest that the efficacy of such off-targeting might be dependent on binding stability. Here, by testing shRNAs and siRNAs of various GC content in different guide strand segments with reporter assays, we establish that weak base pairing in both seed and 3' region  ...[more]

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