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between miRNAs and target sites (
Reinhart
et al.
, 2000
). This pattern holds
true for the hundreds of animal miRNAs now recognized but differs from the
capacity of plant miRNAs to typically base pair perfectly with target mRNAs
(
Bartel, 2009
). Although the inability of animal miRNAs to form antisense
pairs with mRNAs complicates the assignment of miRNAs to specific targets,
several parameters have emerged as useful predictors of these interactions. A
common motif is the ability of the first 2-7nt from the 5
0
end of the miRNA
to perfectly pair with mRNA sequences (
Brennecke
et al.
, 2005; Krek
et al.
,
2005; Lewis
et al.
, 2003, 2005
). This part of the miRNA is known as the
“seed” sequence, and the complementary site in the mRNA is called the
“seed match” (
Lewis
et al.
, 2003
). The requirements for conservation,
3
0
UTR position, and structural accessibility are also often used to restrict
predicted target sites (
Bartel, 2009
). There are examples of targets that lack
seed matches and instead utilize 3
0
supplementary, where extensive comple-
mentarity with the 3
0
end of the miRNA compensates, or centralized pairing
conformations (
Bartel, 2009; Shin
et al.
,2010
).
The first characterized miRNA target sites were all found to reside in
3
0
UTR sequences (
Lee
et al.
, 1993; Moss
et al.
, 1997; Reinhart
et al.
, 2000;
Slack
et al.
, 2000; Wightman
et al.
, 1993
). Computational analyses often
focus on conserved regions in 3
0
UTRs and take into account features like
the number of target sites, their position relative to the stop codon and
polyA signal, structural accessibility and whether they exist in A/U rich
areas, to better predict miRNA target sites (
Bartel, 2009
). Surprisingly, an
experimentally based genome-wide analysis of
C. elegans
Argonaute binding
sites revealed that
35% in 3
0
UTRs of
bound mRNAs (
Zisoulis
et al.
, 2010
). This is consistent with similar
analyses in mammalian cells, where about half of the Argonaute binding
sites were found in coding exon regions (
Chi
et al.
, 2009; Hafner
et al.
,
2010
). While some target sites in coding exons have been shown to confer
miRNA function, the general efficacy of regulation in translated regions of
mRNAs may be reduced compared to that in 3
0
UTRs (
Gu
et al.
, 2009;
Kloosterman
et al.
, 2004
). Recent studies trying to understand the func-
tionality of miRNA target sites in coding regions reveal a synergistic effect,
where there are stronger effects on mRNAs bound by miRNAs in the
3
0
UTR and coding exons, though they are not as strong as the effects when
there are two target sites in the 3
0
UTR (
Fang and Rajewsky, 2011
).
Association of the miRNA complex with a target mRNA results in
downregulation of the protein expression through mechanisms that are not
entirely understood. There is an ongoing debate about whether the primary
mode of regulation is translational repression of the mRNA, or deadenyla-
tion followed by degradation of the mRNA (
Fig. 1.2
;
Djuranovic
et al.
,
2011; Huntzinger and Izaurralde, 2011; Krol
et al.
, 2010
). Original studies
of
lin-14
repression by lin-4 miRNA detected little change in target mRNA
levels or polysome loading and concluded that regulation involved a
50% occur in coding exons and
