Interaction of mRNA 3’ UTRs with miRNA 5’ ends (the so called seed region) for translational repression
is a well known fact and the basis for present day computational models for predicting miRNA targets.
But, recent studies have identified new classes of miRNA target sites located in the coding region
and also in the 5’ UTRs of mRNAs, interacting with the central region or even with the 3’ ends of miRNAs.
We studied all types of known miRNA target sites, including conventional and nonconventional ones,
in a dataset of measured protein fold changes upon miRNA transfections to find the correlation of
different types of target sites with protein fold changes. We found significant correlations for some
non conventional target sites involving miRNA 3' end interactions in the coding region and the 3’ UTR of the target mRNA.
We have developed a model to predict the degree of miRNA target regulation in terms of protein fold changes
from the number of different conventional and nonconventional target sites present in the target.