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Open Access Research article

Deciphering the porcine intestinal microRNA transcriptome

Soroush Sharbati1*, Marc R Friedländer2, Jutta Sharbati1, Lena Hoeke1, Wei Chen23, Andreas Keller4, Peer F Stähler4, Nikolaus Rajewsky2 and Ralf Einspanier1

Author Affiliations

1 Freie Universität Berlin, Institute of Veterinary Biochemistry, Oertzenweg 19b, 14163 Berlin, Germany

2 Max Delbrück Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany

3 Max Planck Institute for Molecular Genetics, Department of Human Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany

4 febit biomed gmbh, Im Neuenheimer Feld 519, 69120 Heidelberg, Germany

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BMC Genomics 2010, 11:275  doi:10.1186/1471-2164-11-275

Published: 30 April 2010

Abstract

Background

While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy.

Results

Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks.

Conclusions

In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.