Biology Reference
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target site play a detectable role in the efficacy of target site recognition,
yet the magnitude of this effect relative to sequence determinants
117
is yet
to be determined.
7.4. Other Determinants
With the availability of sufficiently accurate target prediction methods as
well as relatively large data sets of mRNA expression profiles obtained
after miRNA and siRNA transfection,
118-120
it became possible to ask the
question of what other features may contribute to the efficacy of miRNA
target sites. The relative position of the target site with respect to the
3
UTR boundaries was one of the first such determinants discov-
ered
112,117,121
: target sites that are close, yet not adjacent, to the stop
codon and the poly(A) tail are more strongly conserved and appear to be
more efficient in triggering mRNA degradation. The conservation pro-
file of 3
′
UTRs follows a similar pattern (not shown), suggesting that
miRNAs exert an important pressure on the evolution of 3
′
UTRs, as
argued by Stark
et al
.
122
An interesting question is whether this positional
bias is a reflection of spatial constraints on the RISC interaction with
other complexes involved in translation silencing and mRNA degrada-
tion. Alternatively, the regions close to 3
′
UTR boundaries may provide
the optimal sequence and structure environment for the recruitment of
components necessary for silencing. Grimson
et al
.
117
showed that the
efficacy of target sites correlates with the A/U-richness of their environ-
ments, and Robins and Press
123
′
argued that miRNA targets generally
UTRs. Thus, the local sequence composition, either
through the recruitment of A/U-rich sequence binding proteins or indi-
rectly, through the secondary structure, is a determinant of miRNA
target site efficacy.
Apart from the efficacy of individual sites, many authors have made
the observation that the presence of multiple target sites for an individ-
ual miRNA in the 3
have A/U-rich 3
′
UTR of a given transcript is more indicative of a
functional miRNA-target interaction than the presence of single sites.
Interestingly, some of the best known miRNA targets, such as the hunchback-
like 1
45
and the dauer formation family member 12 transcripts,
targeted by let-7 in
C. elegans
, do indeed have multiple putative miRNA
′
