Research

MicroRNA profiling of the murine hematopoietic system

Silvia Monticelli^1,2*†, K Mark Ansel^1†, Changchun Xiao^1†, Nicholas D Socci^3†, Anna M Krichevsky⁴, To-Ha Thai¹, Nikolaus Rajewsky⁵, Debora S Marks⁶, Chris Sander³, Klaus Rajewsky¹, Anjana Rao¹ and Kenneth S Kosik^4,7

• * Corresponding author: Silvia Monticelli monticel@cbr.med.harvard.edu

• † Equal contributors

Author Affiliations

¹ Department of Pathology, Harvard Medical School, and CBR Institute for Biomedical Research, Boston, MA 02115, USA

² Department of Biology and Genetics of Medical Sciences, Universitá degli Studi di Milano, 20133 Milan, Italy

³ Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA

⁴ Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA

⁵ Center for Functional Comparative Genomics, Department of Biology, New York University, New York, NY 10003, USA

⁶ Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA

⁷ Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA

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Genome Biology 2005, 6:R71 doi:10.1186/gb-2005-6-8-r71

Published: 1 August 2005

Abstract

Background

MicroRNAs (miRNAs) are a class of recently discovered noncoding RNA genes that post-transcriptionally regulate gene expression. It is becoming clear that miRNAs play an important role in the regulation of gene expression during development. However, in mammals, expression data are principally based on whole tissue analysis and are still very incomplete.

Results

We used oligonucleotide arrays to analyze miRNA expression in the murine hematopoietic system. Complementary oligonucleotides capable of hybridizing to 181 miRNAs were immobilized on a membrane and probed with radiolabeled RNA derived from low molecular weight fractions of total RNA from several different hematopoietic and neuronal cells. This method allowed us to analyze cell type-specific patterns of miRNA expression and to identify miRNAs that might be important for cell lineage specification and/or cell effector functions.

Conclusion

This is the first report of systematic miRNA gene profiling in cells of the hematopoietic system. As expected, miRNA expression patterns were very different between hematopoietic and non-hematopoietic cells, with further subtle differences observed within the hematopoietic group. Interestingly, the most pronounced similarities were observed among fully differentiated effector cells (Th1 and Th2 lymphocytes and mast cells) and precursors at comparable stages of differentiation (double negative thymocytes and pro-B cells), suggesting that in addition to regulating the process of commitment to particular cellular lineages, miRNAs might have an important general role in the mechanism of cell differentiation and maintenance of cell identity.