| MicroRNAs(miRNAs), a class of noncoding RNA of approximately 22 nucleotides in length, can regulate gene expression by binding to the region of 3'UTR of the target mRNAs. Increasing evidence indicates that microRNA have been implicated in a variety of critical biological processes, including development, cell differentiation, and oncogenesis. The characterization of miRNA is still a hot academic domain because miRNAs identified so far are far from saturated. MiRNA in mammalian is highly conversative during evolution, not only in highly relative species, but also in widely divergent species. The genome of cow has been completely sequenced and annotated, which provides advantage to search new cow microRNAs and their target genes by computational analysis. Alignment show that cows and humans have similar levels of overall nucleotide diversity, so cow may be served as a model organism for the study of human disease.We apply comutational RNomies and experiment Rnomics to predict and validate miRNA in cow based on sequence conservation of mature miRNAs and their precursor displaying hairpin structure, leading to identification of 289 homology miRNAs.The following is the summarization of our result:1. The loci of all 289 microRNA sequences in genome lie in all 30 chromosomes of genome. Among these miRNAs, 48 in chromosome 21, 20 in chromosome 19 and 19 in chromosomeâ…©. The genomic organization of these candidate miRNA genes is divergent:190 are located in the intergenic regions; 92 in intron regions (49 in sense chain and 43 in anti-sense chain); 2 in exon region; 2 in UTR region and 2 in unknown region. All precursors ranged from 65 to 120 nt in length, with average length of 80 nt.2. Computational analysis showed that a majority of miRNA identified in this work can be folded to the typical stem-loop secondary structure of the miRNA family. Performing RT-PCR assay of 7 miRNAs, we found that several miRNAs have different expression level among different organs, such as miR-130a, miR-134, miR-335, and miR-655. 3. Analysis showed that the 289 homologue miRNA belong to 145 families, and let-7 and miR-17 family have 11 an7 members, respectively. Most of families only have one member, which is different from plant. Members of animal family display multi-copy, closely related or homology.4. Using promoter analysis program, we found that of the 289 miRNA identified in this work, 130 are grouped into 40 clusters controlled by promoter in upstream. Further analysis indicate that duplication, mutation and depletion have happen during evolution.And then, duplication of clusters themselves form distinct paralogous clusters.5. A majority of miRNAs are conserved among animal. Most of miRNAs evolved by local tandem duplication and non-local duplication. Local tandem duplications result in paralogous sequences that are located on the same transcript. Non-local duplications result in paralogous genes or gene clusters on different chromosomes.6. We use miranda for sequence batch processing, 843 potential target in cow has been pretested.A majority of targets are partly matched,which suggest that they may have been translation depression;a few miRNA matched with target completly ,they may cause mRNA degradation. A majority of target involved in almost all cellular processes, for example, development, metabolism, regulatory factor and signal transduction. The most riched GO term is transcriptional factor. Meanwhile, some miRNAs might are involved in processes related with cancer.
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