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Animal microRNAs (miRNAs) regulate gene expression by inhibiting translation and/or by inducing degradation of target messenger RNAs. It is unknown how much translational control is exerted by miRNAs on a genome-wide scale. We used a new proteomic approach to measure changes in synthesis of several thousand proteins in response to miRNA transfection or endogenous miRNA knockdown. In parallel, we quantified mRNA levels using microarrays. Here we show that a single miRNA can repress the production of hundreds of proteins, but that this repression is typically relatively mild. A number of known features of the miRNA-binding site such as the seed sequence also govern repression of human protein synthesis, and we report additional target sequence characteristics. We demonstrate that, in addition to downregulating mRNA levels, miRNAs also directly repress translation of hundreds of genes. Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes.

Nature 473, 337–342 (2011); doi:10.1038/nature10098 Mark Biggin of the Lawrence Berkeley National Laboratory contacted us, noting that our mass-spectrometry-based protein copy number estimates are lower than several literature-based values. We therefore re-analysed the scripts used for data processing, and found a scaling error that occurred during the conversion of normalized protein intensity values into absolute copy number estimates.