Biology Reference
In-Depth Information
gave rise to approximately 800 000 stem-loops. This gives a frequency of
approximately 1 conserved stem-loop every 7500 nucleotides. One
expects that only a small proportion of these represent miRNA precur-
sors, and that additional properties, beyond a stem-loop precursor struc-
ture, distinguish miRNA precursors from other stem-loop-forming
sequences.
One important difference was reported by Bonnet
et al
.
87
By com-
paring the free energy of folding predicted for miRNA precursors with
that predicted for variants whose sequence has been randomized while
preserving the mononucleotide or dinucleotide composition, they found
that miRNA precursors have significantly lower free energy. This indi-
cates an evolutionary pressure on the miRNA precursor sequence, such
as to form stable secondary structures that are presumably necessary for
miRNA biogenesis. Related observations, i.e. that the free energy of fold-
ing normalized by the sequence length
88-90
and additionally by the G/C
content
89,90
is higher for miRNA precursors compared to other stem-
loops, have also been reported. Moreover, miRNA precursors appear to
be robust with respect to mutation,
91
meaning that many of their single-
point mutant neighbors fold into the same secondary structure, but this
does not hold for other sequences that have the same minimum free
energy folds as the miRNA precursors.
6.1.2. Structural constraints
A second important feature of the secondary structure of miRNA precur-
sors is the relative symmetry of the internal loops.
48,92,93
That is, internal
loops tend to involve the same number of nucleotides on the 5
′
as on the
side of the loop. A very recent study of the predicted three-dimensional
structures of miRNA precursors suggests that the reason behind these
initial observations is that these symmetrical loops with particular
nucleotide-nucleotide mismatches do not disturb the docking surface of
the Dicer processing enzyme.
94
Mismatched nucleotides either interact
with a geometry isosteric to Watson-Crick base pairs, or stack inside the
helix, or form bulges behind the docking surface of Dicer, without hin-
dering the binding. In contrast to siRNAs, both strands of which can
generally be incorporated into the RISC complex, miRNA processing
3
′
