Biology Reference
In-Depth Information
target sites. These observations lead to the speculation that miRNAs
may act in a “cooperative”
124
or “coordinated”
125
manner. The mecha-
nism(s) behind this cooperativity remains to be established.
Nonetheless, incorporating these features into miRNA target prediction
programs increases the accuracy of target prediction,
117
even though the
prediction of mRNA changes upon miRNA overexpression remains a
challenging task.
7.5. miRNA Target Prediction Methods
Initially, miRNA target prediction methods attempted to identify
3
UTRs that could form extensive hybrids with miRNAs. To improve
their accuracy, these methods also filtered their predictions using evolu-
tionary conservation.
The first genome-wide target prediction methods to be published
were those of Stark
et al
.,
113
dealing with miRNA target prediction in
D. melanogaster
, and TargetScan,
110
applied to the prediction of mam-
malian miRNA targets. The method of Stark
et al
.
113
used the alignment
tool HMMer
126
to search for 3
′
UTR segments that were complementary
(allowing for G-U pairs) to the first eight nucleotides at the 5
′
end of
miRNAs. These segments were extended to the length of the miRNA
plus another five nucleotides, and Mfold
127
was then used to predict the
free energy of folding between the putative site and the miRNA. The
score of the site was the
Z
-value of its value relative to 10 000 random
target sequences. The score of the 3
′
′
UTR was the number of sites with
a
Z
-value
3.
TargetScan used a fairly similar approach. Initially, 3
≥
UTR sequences
were searched for the presence of segments that had perfect
Watson-Crick complementarity to nucleotides 2-8 of miRNAs, a region
which was referred to as the “seed”. The complementarity was then
extended in both directions, allowing G-U pairs, but stopping at mis-
matches. Finally, the 3
′
UTR regions obtained in the previous steps were
extended to 35 nucleotides upstream of the “seed match”, the RNAfold
program
128
′
end of the
miRNA to the putative target site, and a final hybridization energy
between the miRNA and the putative target site constructed in this
was used to predict the hybridization of the 3
′
