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Microarray analysis of microRNA expression in the developing mammalian brain

Eric A Miska1, Ezequiel Alvarez-Saavedra1, Matthew Townsend24, Akira Yoshii2, Nenad Šestan3, Pasko Rakic3, Martha Constantine-Paton2 and H Robert Horvitz1*

  • * Corresponding author: H Robert Horvitz

  • † Equal contributors

Author affiliations

1 Howard Hughes Medical Institute, Department of Biology and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

2 Departments of Biology and Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

3 Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA

4 Center for Neurologic Diseases, Harvard Medical School, Boston, MA 02115, USA

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Citation and License

Genome Biology 2004, 5:R68  doi:10.1186/gb-2004-5-9-r68

Published: 31 August 2004



MicroRNAs are a large new class of tiny regulatory RNAs found in nematodes, plants, insects and mammals. MicroRNAs are thought to act as post-transcriptional modulators of gene expression. In invertebrates microRNAs have been implicated as regulators of developmental timing, neuronal differentiation, cell proliferation, programmed cell death and fat metabolism. Little is known about the roles of microRNAs in mammals.


We isolated 18-26 nucleotide RNAs from developing rat and monkey brains. From the sequences of these RNAs and the sequences of the rat and human genomes we determined which of these small RNAs are likely to have derived from stem-loop precursors typical of microRNAs. Next, we developed a microarray technology suitable for detecting microRNAs and printed a microRNA microarray representing 138 mammalian microRNAs corresponding to the sequences of the microRNAs we cloned as well as to other known microRNAs. We used this microarray to determine the profile of microRNAs expressed in the developing mouse brain. We observed a temporal wave of expression of microRNAs, suggesting that microRNAs play important roles in the development of the mammalian brain.


We describe a microarray technology that can be used to analyze the expression of microRNAs and of other small RNAs. MicroRNA microarrays offer a new tool that should facilitate studies of the biological roles of microRNAs. We used this method to determine the microRNA expression profile during mouse brain development and observed a temporal wave of gene expression of sequential classes of microRNAs.