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

Abstract

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.