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A custom microarray platform for analysis of microRNA gene expression

Nature Methods volume 1, pages 47–53 (2004)Cite this article

Abstract

MicroRNAs are short, noncoding RNA transcripts that post-transcriptionally regulate gene expression. Several hundred microRNA genes have been identified in Caenorhabditis elegans, Drosophila, plants and mammals. MicroRNAs have been linked to developmental processes in C. elegans, plants and humans and to cell growth and apoptosis in Drosophila. A major impediment in the study of microRNA function is the lack of quantitative expression profiling methods. To close this technological gap, we have designed dual-channel microarrays that monitor expression levels of 124 mammalian microRNAs. Using these tools, we observed distinct patterns of expression among adult mouse tissues and embryonic stem cells. Expression profiles of staged embryos demonstrate temporal regulation of a large class of microRNAs, including members of the let-7 family. This microarray technology enables comprehensive investigation of microRNA expression, and furthers our understanding of this class of recently discovered noncoding RNAs.

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Figure 1: Validation of the labeling method.
Figure 2: Sensitivity and specificity of microRNA microarrays.
Figure 3: Expression data from seven adult mouse tissues, ES cells, embryoid bodies (EB) and four mouse embryo stages.

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Acknowledgements

Cluster and Treeview software were developed by M. Eisen and generously distributed by Stanford University. The authors acknowledge the UNC Genomics and Microarray Core Facility for assisting in microarray production. The authors thank G. Hannon, Y. Xiong, M. Carmell, and members of the Hammond laboratory for critical reading of the manuscript and discussion of the project. S.M.H. is a General Motors Cancer Research Foundation Scholar.

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Author notes

  1. Joel Parker

    Present address: Constella Group, Inc., 2605 Meridian Parkway, Durham, North Carolina, 27713, USA

Authors and Affiliations

  1. Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, 27599, North Carolina, USA

    J Michael Thomson & Scott M Hammond

  2. Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599, North Carolina, USA

    Joel Parker, Charles M Perou & Scott M Hammond

  3. Department of Genetics, University of North Carolina, Chapel Hill, 27599, North Carolina, USA

    Charles M Perou

  4. Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, 27599, North Carolina, USA

    Charles M Perou

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Corresponding author

Correspondence to Scott M Hammond.

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Supplementary information

Supplementary Fig. 1

MicroRNA sequences used for microarray design. (PDF 53 kb)

Supplementary Fig. 2

Normalization of microRNA microarrays. (PDF 66 kb)

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Thomson, J., Parker, J., Perou, C. et al. A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1, 47–53 (2004). https://doi.org/10.1038/nmeth704

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