Abstract
BackgroundWhile 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.ResultsHere, 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.ConclusionsIn 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.
Highlights
While more than 700 microRNAs are known in human, a comparably low number has been identified in swine
As a proof of principle that deep sequencing can be used to discover hundreds of novel miRNAs from a single sample, we have introduced a method based on downstream sequence analysis using the algorithm miRDeep to detect ~ 200 previously unannotated canine miRNAs [18]
Deep sequencing unravels the expression of more than 300 potential porcine intestinal miRNAs We have applied deep sequencing to analyze the expression of regulating miRNAs in the porcine intestine
Summary
While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. During evolution more and more miRNA families were added to metazoan genomes and once incorporated into regulatory networks, few shifts of the mature sequence have occurred. These observations led to the hypothesis that morphological complexity is in part directed by the acquisition of new miRNA families during animal phylogeny [6,7]. According to miRBase Release 14.0 [8], the number of noted human and murine miRNAs exceeds 700 and 500, respectively. Beside these species, the coverage of the miRNAome from other mammals e.g. pig remains scarce
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