Information Technology Reference
In-Depth Information
The model the
TP gene, which initially lacks IESs, aligns with a loop of AT-
rich spacer DNA (Figure 9.28). A series of recombinations between the gene
and the AT-rich loop creates MDSs 1-12, connecting MDSs 1, 3, 5, 7, 9, and 11
in one series, and MDSs 2, 4, 6, 8, 10, and 12 in another series. A recombination
between two segments of the AT-rich loop creates IES 6, connecting MDS 11
with MDS 2. Nonscrambled MDSs 12, 13, and 14 are created as separate events
by insertion of two IESs either before or after the main set of recombinations.
The model can be applied to the DNA
pol
α
α
gene as well.
TEMPLATE-GUIDED MODEL OF RECOMBINATION
IN GENE ASSEMBLY
The pointers in MDSs that flank IESs range in length from 3 to 8 basepairs
and average 4 basepairs in the case of those IESs separating two numerically
consecutive MDSs. These include not only IESs in nonscrambled genes but also
some IESs in genes in which some of the MDSs are scrambled. For example,
IES 1 in the actin I gene of
Sterkiella nova
is flanked by MDSs 3 and 4 (i.e., they
are nonscrambled relative to each other; the incoming and outgoing pointers
P4 in these MDSs is 4 bp. However, the pointers in MDSs that are scrambled
relative to each other range from 7 to 19 bp, with an average of 11 bp. The
reason for the longer pointers in scrambled MDSs is surely significant, but it is
not understood.
Clearly, in the case of nonscrambled MDSs, the pointers are too short to
specify unambiguously the correct alignment of the pointers for recombina-
tional excision of the IESs. A pointer of 4 bp (the average length for nonscram-
bled MDSs) will occur by chance on average every 4
4
, or 256 bp. Thus, the
probability is high that a copy of a 4-bp pointer will occur within an IES itself
or in one or both MDSs within a few hundred basepairs of the IES. How are
the correct copies of the pointer chosen for alignment and recombination? A
specific example of the problem is the pair of 3-bp pointers P7 that flank IES
6 (separating nonscrambled MDSs 6 and 7) in the actin I gene of
Sterkiella
histriomuscorum
(see Figure 9.19). This 3-bp pointer sequence (AGT) occurs
five times within the IES, again in MDS 7, 8 bp downstream of the IES, and in
MDS 6, just 44 bp upstream of the IES, creating many possibilities for misiden-
tification of pointers. Misidentification of the correct copies of pointers in the
case of scrambled MDSs might seem to be much less of a problem because the
pointers are longer. The shortest pointer, 6 bp, will occur by chance on average
once every 4096 bp. However, members of some pointer pairs must be brought
into alignment from distances much greater than 4096 bp (e.g., the pointers in
the eight MDSs of the DNA
pol
gene that are in a completely different location
in the genome), leaving open the possibility for incorrect identification of the
correct copies of pointers.
α
