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Lessons from Nature: microRNA-based shRNA libraries

Abstract

Loss-of-function genetics has proven essential for interrogating the functions of genes and for probing their roles within the complex circuitry of biological pathways. In many systems, technologies allowing the use of such approaches were lacking before the discovery of RNA interference (RNAi). We have constructed first-generation short hairpin RNA (shRNA) libraries modeled after precursor microRNAs (miRNAs) and second-generation libraries modeled after primary miRNA transcripts (the Hannon-Elledge libraries). These libraries were arrayed, sequence-verified, and cover a substantial portion of all known and predicted genes in the human and mouse genomes. Comparison of first- and second-generation libraries indicates that RNAi triggers that enter the RNAi pathway through a more natural route yield more effective silencing. These large-scale resources are functionally versatile, as they can be used in transient and stable studies, and for constitutive or inducible silencing. Library cassettes can be easily shuttled into vectors that contain different promoters and/or that provide different modes of viral delivery.

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Figure 1: Structure of shRNAmir.
Figure 2: Schematics of first- and second-generation library vectors.
Figure 3: Mating scheme for pSM2 library clones.

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Correspondence to Gregory J Hannon.

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Competing interests

S.J.E. and G.J.H. are consultants for Open Biosystems, and K.C., S.J.E. and G.J.H. receive royalties from the sales of library materials.

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Chang, K., Elledge, S. & Hannon, G. Lessons from Nature: microRNA-based shRNA libraries. Nat Methods 3, 707–714 (2006). https://doi.org/10.1038/nmeth923

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