Biology Reference
In-Depth Information
elements found in the 3
UTRs of transcripts encoding Notch pathway
basic helix-loop-helix (bHLH) repressors and Bearded family proteins
in
D. melanogaster
are complementary to the 5
′
end of various
miRNAs. A subsequent experimental study in which mutations were
introduced individually in each of the nucleotides of the miRNA bind-
ing site of a reporter transcript
103
confirmed that mutations in
nucleotides complementary to positions 2-8 of the miRNA are most
deleterious for the miRNA-induced translation inhibition. On the com-
putational side, Lewis
et al
.
110
′
analyzed the conservation of subse-
quences of human 3
ends
and found that they are considerably more conserved than random sub-
sequences of the same length, indicating that miRNAs have many
mRNA targets that are conserved in evolution. These computational
studies do not imply that perfect complementarity to the 5
′
UTRs that are complementary to miRNA 5
′
end of the
miRNA is indispensable for function
111
; rather, they indicate that the
accuracy of prediction of seed-complementary sites should be higher
than the accuracy of prediction of sites with imperfect pairing in the
5
′
′
region of the miRNA.
81,112
7.3. Structural Determinants
Given that the targets of miRNAs are mRNAs, it was expected that this
interaction is governed by RNA-RNA interaction rules, which is why the
first miRNA target prediction programs
108,110,113
took into account the
hybridization energy between miRNA and putative target sites.
Additional indication that the hybridization between miRNAs and target
sites is important for target recognition came from the experimental
study of Brennecke
et al
.,
103
who defined three types of miRNA target
sites; one of these is the “3
′
-compensatory” type, in which relatively poor
complementarity of the 5
end of the miRNAs to the target sites appears
to be compensated by strong complementarity of the 3
′
end. More
recently, Lewis
et al
.
104
showed that a better specificity of miRNA target
prediction can be achieved by considering only the evolutionary conser-
vation of miRNA-complementary motifs. The role of structural determi-
nants is currently under debate. Some studies
114-116
do indicate that the
secondary structure formation and, in particular, the accessibility of the
′
