A novel putative miRNA target enhancer signal

Abstract

It is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific. Recent experiments suggest further context signals involved in miRNA target site recognition and regulation. Here, we present a novel GC-rich RNA motif downstream of experimentally supported miRNA target sites in human mRNAs with no similarity to previously reported functional motifs. We demonstrate that the novel motif can be found in at least one third of all transcripts regulated by miRNAs. Furthermore, we show that motif occurrence and the frequency of miRNA target sites as well as the stability of their duplex structures correlate. The finding, that the novel motif is significantly associated with miRNA target sites, suggests a functional role of the motif in miRNA target site biology. Beyond, the novel motif has the impact to improve prediction of miRNA target sites significantly.

Figure 1. RNA motif.

Detected novel miRNA target context sequence motif downstream of experimentally supported human miRNA target sites motif as sequence logo plot. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each nucleic acid at that position. Here the motif calculated from the non-redundant sequence set with maximum 65% allowed homology is shown. Noteworthy are the overall high GC content, the strong increase of cytosine nucleotides around the motif position 22 and a peak of guanine residues around motif positions 39.

Figure 2. Percentage of distinct 3′-UTR transcripts having one or more miRNA target sites predicted.

The folding energy indicates the stability of the RNA hetero duplex of the miRNA with the RNA binding site on the mRNA. Lower energy values indicate a stronger binding and are usually used as a parameter to filter miRNA target site predictions. Here, it can be seen that of the transcripts with the novel motif significantly more have at least one miRNA target site. The difference between transcripts-with-motif and transcripts-without-motif is shown as delta line. With increased stringent target site filtering, transcripts-with-motif show significantly more frequent at least one miRNA target site. Additionally, this indicates that the miRNA target site predictions in transcripts-with-motif have stronger miRNA:mRNA binding duplex structures on average.

Figure 3. Number of predicted miRNA targets sites in transcripts with and without motifs.

We conform that with increasing energy threshold the likelihood of predicted miRNA target sites decreases. Beyond, it can be seen that the amount of predicted miRNA target sites normalized by the sequence length is higher for transcripts-without-motif at first. However, regarding predictions that are supposed to be more stable (energy values get higher absolute values), more hits can be found in transcripts-with-motif.