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Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs

Abstract

MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression in plants and animals1,2. To investigate the influence of miRNAs on transcript levels, we transfected miRNAs into human cells and used microarrays to examine changes in the messenger RNA profile. Here we show that delivering miR-124 causes the expression profile to shift towards that of brain, the organ in which miR-124 is preferentially expressed, whereas delivering miR-1 shifts the profile towards that of muscle, where miR-1 is preferentially expressed. In each case, about 100 messages were downregulated after 12 h. The 3′ untranslated regions of these messages had a significant propensity to pair to the 5′ region of the miRNA, as expected if many of these messages are the direct targets of the miRNAs3. Our results suggest that metazoan miRNAs can reduce the levels of many of their target transcripts, not just the amount of protein deriving from these transcripts. Moreover, miR-1 and miR-124, and presumably other tissue-specific miRNAs, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans.

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Figure 1: Tissue-specific gene expression rankings for downregulated genes.
Figure 2: Over-represented motifs in the 3′ UTRs of downregulated genes.
Figure 3: Microarray analysis of the effects of miRNA mutations.
Figure 4: MicroRNA-directed repression of renilla luciferase reporter genes bearing 3′ UTR segments from predicted target genes.

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Acknowledgements

Thanks to S. Baskerville, M. Cleary and P. Sharp for comments on the manuscript, C. Armour, S. Bartz, J. Burchard, G. Cavet, D. Haynor, A. Jackson, M. Pellegrini, E. Schadt and Y. Wang for their assistance, the Rosetta Gene Expression Laboratory for microarray work, M. Jones-Rhoades for primer design, and W. Johnston for plasmid construction.

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Correspondence to Lee P. Lim.

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Supplementary information

Supplementary Discussion

Analysis of overlaps with computational predictions. (DOC 45 kb)

Supplementary Note

Sequences cloned into reporter vectors. (DOC 53 kb)

Supplementary Figure 1

Quantitative northern blot analysis of miR-1 and miR-124 expression. (PDF 359 kb)

Supplementary Figure 2

Tissue analysis for mutant microRNAs. (PDF 28 kb)

Supplementary Figure 3

Expected and observed seed match counts in different regions of miR-1 or miR-124 downregulated genes. (PDF 8 kb)

Supplementary Figure 4

p-values of enrichment for hexamers complementary to miR-124 in the 3' UTRs of the miR-124 downregulated genes. (PDF 8 kb)

Supplementary Figure 5

Motif and tissue analysis for miR-373. (PDF 43 kb)

Supplementary Table 1

Genes downregulated by miR-1 at a p-value < 0.001 at both 12 and 24 h. (DOC 209 kb)

Supplementary Table 2

Genes downregulated by miR-124 at a p-value < 0.001 at both 12 and 24 h. (DOC 342 kb)

Supplementary Table 3

Hexamers enriched in the 3' UTRs of the downregulated sets. (DOC 52 kb)

Supplementary Table 4

Genes downregulated by miR-373 at a p-value < 0.001 at both 12 and 24 h. (DOC 155 kb)

Supplementary Methods

This file contains MIAME (Minimum Information About a Microarray Experiment) methods data. (DOC 44 kb)

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Lim, L., Lau, N., Garrett-Engele, P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005). https://doi.org/10.1038/nature03315

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