Probing miRNAs with microarrays: tissue specificity and functional inference

TOMAS BABAK^{1, 2}, WEN ZHANG^{1, 2}, QUAID MORRIS¹, BENJAMIN J. BLENCOWE^{1, 2}

and TIMOTHY R. HUGHES^{1, 2*}

¹Banting and Best Department of Medical Research, 112 College St., Toronto, ON M5G 1L6 Canada

²Department of Medical Genetics and Microbiology, 10 Kings College Circle, Toronto, ON M1R 4F9 Canada

*To whom correspondence should be addressed:

t.hughes@utoronto.ca

416-946-8260

FAX: 416-978-8528

Abstract:

MicroRNAs (miRNAs) are short, stable, noncoding RNAs involved in post-transcriptional gene silencing via hybridization to mRNA. Few have been thoroughly characterized in any species. Here, we describe a method to detect miRNAs using micro-arrays, in which the miRNAs are directly hybridized to the array. We used this method to analyze miRNA expression across 17 mouse organs and tissues. More than half of the 78 miRNAs detected were expressed in specific adult tissues, suggesting that miRNAs have widespread regulatory roles in adults. By comparing miRNA levels to mRNA levels determined in a parallel microarray analysis of the same tissues, we found that the expression of target mRNAs predicted on the basis of sequence complementarity is unrelated to the tissues in which the corresponding miRNA is expressed.

Supplementary Data:

Supplementary Figures
Array Design and ncRNA Expression Data
- Description
- The Data (excel)
Miranda (Enright et al. 2003) and Targetscan (Lewis et al. 2003) Predicted Targets
Expression Data for Previously Published Targets (Lewis et al. 2003)
SVM Predictions
- Description
- SVM Predictions (text)
miRNA - Coregulated Genes and their Functional Enrichments