Identification of differentially expressed microRNAs in placentas of cloned and normally produced calves by Solexa sequencing

Aberrant gene expression caused by aberrant nuclear reprogramming results in developmental abnormalities in cloned animals and ultimately their death. MicroRNAs (miRNAs), a family of ∼22 nucleotide, non-coding, single-stranded RNA molecules, are considered as key regulators of gene expression. Numerous miRNAs and their expression patterns have been identified in various species. However, the significance of miRNAs in developmental abnormalities in cloned animals is unclear. Small RNA libraries were generated from the placentas of cloned (somatic cell nuclear transfer, SCNT) and normally produced (control) calves. A total of 18,815,541 clean reads were obtained from the SCNT library and 19,329,352 from the control library. In total, 430 conserved bovine miRNAs were identified in bovine placenta. Furthermore, the family, expression predominance, and base substitution of the conserved miRNAs were also analyzed. We found 135 conserved miRNAs that were differentially expressed significantly between the two samples, which suggest that these miRNAs may affect developmental abnormalities in cloned cattle and ultimately their death. The miRNA target prediction, gene ontology, and pathway analysis for these target genes were also carried out. The present study expands the collection of bovine miRNAs and could initiate further studies on the functions of miRNAs in developmental abnormalities and death in cloned animals.