Systemic comparison of repression activity for miRNA and siRNA associated with different types of target sequences

Most miRNA target sites are determined by Watson-Crick pairing via the seed region (positions ∼2-7nt of the mature miRNA). The binding sites of target mRNAs are categorized primarily as 7mer-m8, the 7mer-1A and the 8mer sites. This study analyzed post-transcriptional repression as a function of associations among various seed/target sequences. The target sequence of miR-155 from TP53INP1 was modified such that their various monomers and dimers could be inserted into the 3'UTR of a reporter gene for monitoring repression activity of miR-155. Results revealed that the level of repression could be ordered as follows: perfect-matched target≫dimeric targets≫monomeric targets. For dimeric targets, the order is 2×8mer>2×7mer-m8>2×7mer-1A. Fold repression of 8mer+7mer-1A lay between 2×8mer and 2×7mer-1A. A mismatch in one seed dramatically decreasing repressive activity of the dimer. This indicated that the degree of repression could be synergistically enhanced through the cooperation of the two miRISC-loaded monomers. The siRNA-155 (siRNA carrying miR-155 sequence) elicited higher repressive activity than miR-155, as they bound to the perfectly matched target. However, strong repression of miR-155 and siRNA-155 with a perfectly matched target was due primarily to translational attenuation. Cleavage/degradation of the target mRNA was not a major cause of the observed repression.