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We used a combination of RIP-Seq analysis of small RNA and mRNA to identify miRNA and their potential target mRNAs in a colon cancer cell line. We recovered RNAs co-immunoprecipitated with Ago1 or Ago2 and subjected them for massively-paralleled small RNA and mRNA Sequencing. Identified miRNAs and mRNAs were further associated with each other by using in silico target predictions. We identified the associations between 90, yy and 83 miRNAs 1161, yy and 1742 mRNAs in Ago1, Ago2 and both, respectively. We found that miRNAs were frequently employed both in Ago1 and Ago2, while their associated mRNAs were selectively associated with either Ago1 or Ago2. We also conducted the similar analysis using the cells cultured in hypoxia and identified hypoxia induced miRNA-mRNAs associations. Again, most of the hypoxia-induced miRNAs were associated with both Ago1 and Ago2, while the mRNAs were associated with either of them. The associations identified in the respective complexes have different characteristics. Namely, Ago1 were associated with genes of constitutive functions, via relatively weak associations, and seemed to have moderate translational consequences. On the other hand, Ago2 were frequently associated with genes playing roles in dynamic response to environmental changes, via strong interactions, and seemed to have strong translational repressions. miRNA-mRNA associations in the respective complexes may have divergent biological relevance as well as distinct interaction machinery. |