title: Deciphering the porcine intestinal microRNA transcriptome.
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.
authors.affiliation: Freie Universität Berlin, Institute of Veterinary Biochemistry, Oertzenweg 19b, 14163 Berlin, Germany. sharbati@zedat.fu-berlin.de
authors.forename: Soroush
authors.initials: S
authors.lastname: Sharbati
authors.forename: Marc R
authors.initials: MR
authors.lastname: Friedländer
authors.forename: Jutta
authors.initials: J
authors.lastname: Sharbati
authors.forename: Lena
authors.initials: L
authors.lastname: Hoeke
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Andreas
authors.initials: A
authors.lastname: Keller
authors.forename: Peer F
authors.initials: PF
authors.lastname: Stähler
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Rajewsky
authors.forename: Ralf
authors.initials: R
authors.lastname: Einspanier
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D007413:Intestinal Mucosa / Q000378:metabolism*; D035683:MicroRNAs / Q000235:genetics*; D017423:Sequence Analysis, RNA; D034421:Sus scrofa / Q000235:genetics*
chemical_list: D035683:MicroRNAs