Biomedical Engineering Reference
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repression (Azzouzi et al.
2011
; Lal et al.
2009
). The type of seed match how-
ever, remains central to the scoring systems of many of the algorithms mentioned
later in this chapter (Sect. 3.3).
The most frequently occurring type of seed regions are known as canonical target
sites and are broadly defined by continuous base pairing spanning 7 or 8 nucleotides.
These site types can be further characterised by a match at position 8 (
7mer-m8
site
), a 7 nucleotide match with binding to an adenosine at position 1 (
7mer-A1 site
),
and matching either any base at position 8 or an adenosine matched at position 1
at the miRNA 5
end (
8mer site
) (Bartel
2009
). Studies have demonstrated that
an adenosine at position 1 (complementary or non-complementary) increases down
regulation of the target in comparison to other target site types (Baek et al.
2008
;
Nielsen et al.
2007
). The presence of adenosines around the seed region seems to be
conserved (Lewis et al.
2005
) and is thought to be important for recognition by the
RNA induced silencing complex (RISC).
Another class of seed region types can be categorised by an additional 4-5 base
complementarity with the target mRNA towards the miRNA 3
end (Bartel
2009
).
These types of target recognition have either a perfect match to the seed region
(
3
-supplementary
) or correct for a mismatch in the seed region (
3
-compensatory
).
Binding of nucleotides at positions 13-16 of the mature miRNA seems to provide
optimum down regulation of targets (Grimson et al.
2007
). The final seed type is
termed “marginal” and is defined by only 6 nucleotide matches with the seed region
(
6mer site
). Base pairing can begin at position 2 or position 3 of the miRNA. Those
algorithms requiring perfect Watson Crick base pairing with the seed region in order
to decrease the false positive rate would therefore ignore these marginal seeds (Bartel
2009
).
3.2.2
mRNA Target Site Location and Abundance
The vast majority of metazoan miRNA binding sites reside within the 3
UTR of the
target transcript. The first miRNAs discovered, lin-4 and let-7 in
C. elegans
, both
bind to sites within the 3
UTR of their respective targets (Lee et al.
1993
; Reinhart
et al.
2000
). The presence of multiple target sites for one or more miRNAs within
the 3
UTR tends to increase miRNA induced repression. In addition, if these sites
are within 13-35 bases of each other they can act in unison to further downregulate
target translation (Brennecke et al.
2005
; Saetrom et al.
2007
). Target gene sites
can be distributed toward both ends of the 3
UTR. The location of the target site
along with surrounding sequence composition of the target site seems to affect the
degree of miRNA regulation. For instance, characteristics of target sites including
lying within 15 nt of the stop codon, away from the centre of long UTRs, near
coexpressed miRNAs and close to AU rich regions, tends to increase effectiveness
(Grimson et al.
2007
). Kertesz et al. provided evidence of the importance of target site
context, demonstrating the impact of target site accessibility and mRNA secondary
structure on the efficiency of translation repression via miRNA. The importance of
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