In silico identification of conserved microRNAs and their targets in bovine fat tissue

MicroRNAs (miRNAs) represent a newly identified class of non-protein-coding ~22 nt small RNA which plays important roles in multiple biological processes by degrading targeted mRNA or repressing mRNA translation. Here we present EST (expressed sequence tags)-based and GSS (Genomic Survey Sequences)-based combined approach for the detection of conserved miRNAs of cattle. A total of 20 conserved miRNAs that belong to 18 miRNA families were detected following a range of filtering criteria; their functions were further predicted and analyzed. To confirm our prediction, a miRNA-detecting microarray was designed with probes complementary to previously known mature miRNA sequences from 131 organisms. After hybridizing with small RNAs extracted from beef cattle subcutaneous fat tissue, 219 (32.30%) miRNAs were detected in the 679 known Bos taurus miRNAs and all the miRNAs predicted above were also detected. Conformation of 22 most abundant miRNA expression by qRT-PCR indicated that they were highly accumulated not only in subcutaneous fat tissue but also in intramuscular fat tissue. Bioinformatics of KEGG pathway analysis suggested that 4 differential expression miRNAs (miR-143, miR-145, miR-2325c and miR-2361) involved in different pathways and target genes may regulate the fat deposition differently. Taken together, our results expand the number of known bovine miRNAs and provide a thorough account of the miRNA transcriptome in bovine adipose tissue.