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Cell-type-specific signatures of microRNAs on target mRNA expression

Sood, Pranidhi, Krek, Azra, Zavolan, Mihaela, Macino, Giuseppe, Rajewsky, Nikolaus·2006·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0511045103
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Abstract

Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue profiles has not been systematically elucidated. Here, we show that predicted human mRNA targets of several highly tissue-specific miRNAs are typically expressed in the same tissue as the miRNA but at significantly lower levels than in tissues where the miRNA is not present. Conversely, highly expressed genes are often enriched in mRNAs that do not have the recognition motifs for the miRNAs expressed in these tissues. Together, our data support the hypothesis that miRNA expression broadly contributes to tissue specificity of mRNA expression in many human tissues. Based on these insights, we apply a computational tool to directly correlate 3′ UTR motifs with changes in mRNA levels upon miRNA overexpression or knockdown. We show that this tool can identify functionally important 3′ UTR motifs without cross-species comparison.

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  • miR-1 is highly prevalent in the heart and skeletal muscle, whereas predicted targets of miR-1 are expressed at significantly lower levels in heart and skeletal muscle compared to other tissues.

    “For example, miR-1 is highly prevalent in the heart and skeletal muscle, whereas the predicted targets of miR-1 are expressed at significantly lower levels in heart and skeletal muscle compared to other tissues (Sood et al. 2006).”

    From MicroRNA expression in the adult mouse central nervous system (2008) · cites this paper as Sood et al. 2006

  • Previous computational analyses of microarray data have shown that predicted mRNA targets of several highly tissue-specific miRNAs are expressed at significantly lower levels in the same tissues compared to tissues where such miRNAs are not expressed.

    “Previous computational analyses of microarray data have shown that predicted mRNA targets of several highly tissue-specific miRNAs are expressed at significantly lower levels in the same tissues compared to tissues where such miRNAs are not expressed (Farh et al. 2005;Sood et al. 2006).”

    From MicroRNA expression in the adult mouse central nervous system (2008) · cites this paper as Sood et al. 2006

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Cited by

Sorted by citations

Authors
Sood, P., Krek, A., Zavolan, M., Macino, G., & Rajewsky, N.
Affiliations
  • *Center for Comparative Functional Genomics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003;
  • Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland; and
  • Dipartimento di Biotecnologie Cellulari ed Ematologia, Universita di Roma La Sapienza, Viale Regina Elena 324, 00161 Rome, Italy
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2006-02-13
Volume
103
Issue
8
Pages
2746-2751
ISSN
  • 0027-8424
  • 1091-6490
DOI
10.1073/pnas.0511045103
Cited by
547
References
3
Language
en

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