Biomedical Engineering Reference
In-Depth Information
C G
U
A
U
A
C
C
A
A
U
C
G
A
A
A
A
A
C
A
G
U
U
U
U
A
G
A
G
U
A
U
U
U
A
C
U
C
C
U
U
C
A
A
G
A
G
C
A
U
G
A
A
C
G
U
U
U
C
U
U
A
G
A
G
A
A
U
U
U
U
A
A
A
A
A
U
U
G
U
G
A
U
U
A
C
U
G
A
U
U
G
U
U
G
A/U
rich
stem
C
G
G
U
U
A
A
A
A
A
A
C
C
U
U
G
C
G
C
U
A
A
A
A
U
A
U
C
A
A
C
U
A
C
A
G
U
U
A
U
A
A
C
U
G
C
A
C
A
C
U
U
C
U
A
U
G
C
C
U
U
C
A
A
C
C
U
G
A
U
G
U
U
C
U
U
U
U
C
G
G
A
G
A
G
C
G
A
G
U
A
C
C
G
A
G
C
C
G
A
A
U
U
G
C
U
A
U
U
U
C
U
U
A
C
G
C
G
A
G
C
A
U
C
U
A
A
G
A
U
C
U
G
A
U
U
U
A
U
C
U
A
G
C
G
G
U
C
C
C
C
C
G
U
U
G
C
C
A
G
U
A
U
C
U
C
U
U
U
C
U
C
U
A
A
A
U
U
A
A
G
fs(1)K10
U
C
U
A
G
G
U
G
U
G
C
A
I Factor
U
U
U
G
A
A
G
U
G
hairy
A
A
U
A
A
A
U
U
U
G
A
A
C
A
U
U
C
U
U
U
C
C
C
U
C
U
U
G
A
U
A
U
U
A
C
U
U
A
G
U
G
A
C
G
U
U
U
A
A
U
U
C
U
G
C
G
A
A
U
A
A
G
A
A
U
C
C
A
U
C
G
gurken
G2
Orb
bcd
Fig. 11.2
Secondary structure predictions for known
cis
-acting signals in
Drosophila
oocytes/
embryos. Each signal is necessary and sufficient to localise the RNA. The
dashed box
around
fs(1)
K10
indicates a purine (A/U) rich helical stem, allowing specific recognition by transport particle
components. The
bicoid
signal is part of a larger sequence mapped that includes several putative
cis
-acting signals
element has been mapped to a 121 nt region in the 3¢ UTR containing two important
stem-loop secondary structures (Bullock et al.
2003
). In yeast, the localisation signal
of b
-actin
mRNA has been mapped to 54 nt and contains a tandem repeat of ACACCC
recognised by Zbp1 (Kislauskis et al.
1994
; Ross et al.
1997
) .
Ash1
mRNA has been
mapped to find four localisation signals in the coding region and 3¢ UTR, each of
which localises
Ash1
to the bud tip of dividing yeast cells (Chartrand et al.
1999
;
Gonzalez et al.
1999
). A spatial arrangement of two cytosine nucleotides within the
signals was shown to be required for localisation, and further RNAs containing the
motif were found computationally using MC-Search (Olivier et al.
2005
) .
11.2.3
RNA
Cis
-Acting Signals
RNA folds to form secondary structures, which then assemble into tertiary structures.
RNA secondary structure is built on canonical Watson-Crick (A:U, U:A, G:C, C:G)
and non-canonical (e.g. G:U, G:A, see Fig.
11.3
) pairings between bases. The RNA
can either be double stranded, when there are complimentary base pairings across
the strands, or single stranded, when there are no base pairings made. The base pair-
ings allow a wide range of structures, including helices, loops, bulges, internal loops
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