Biology Reference
In-Depth Information
distribution pattern of
Alu
sequences in the genome is that procedures which screen
for these repeats in genomic DNA clones will preferentially locate gene sequences.
SINEs have a long evolutionary history, being present in all vertebrate classes
as well as being found in molluscs (Gilbert and Labuda, 1999). SINEs in verte-
brate genomes include various types of DNA transposable element such as
Tiggers
and
mariners
which are characterized by the possession of terminal inverted
repeats and target site duplications evident as flanking direct repeats (Smit and
Riggs, 1996; Robertson and Martos, 1997). The
Tigger
element closely resembles
pogo
, a DNA transposon in
Drosophila
. Most copies of the
mariner
family of trans-
posable elements, of which there are probably more than 1000 in the human
genome, probably originated between 80 and 50 Myrs ago (Robertson and
Zumpano, 1997; Robertson and Martos, 1997). In addition, the MIR transposable
element which has a simple tRNA-like internal polymerase III promoter, was
amplified to several hundred thousand copies before the adaptive radiation of the
mammals (Murnane and Morales, 1995; Smit and Riggs, 1995).
LINE elements.
Some 10
5
copies of long interspersed repeat elements (LINES)
are present in the human genome (Hwu
et al
., 1986). LINES are derived from
polII transcripts and account for perhaps 2-3% of the total DNA complement
(reviewed by Skowronski and Singer, 1986; Singer
et al
., 1993). LINE elements
have been found in all mammalian species so far examined and may be traced
back to an ancestral LINE element that originated before the adaptive radiation
of mammals (Furano and Usdin, 1995). Human LINE elements vary in size from
as little as 60 bp up to 6-7 kb; about 95% are truncated at their 5
ends but they
mostly appear to contain the same 3
sequences as well as a poly(A) tail of variable
length (
Figure 1.8
). Each individual LINE element differs from the consensus
sequence (Scott
et al
., 1987) by ~13% although many exhibit internal deletions
and rearrangements. The majority of human LINE elements appear to have been
generated within the last 30 Myrs (Scott
et al
., 1987).
0
1
2
3
4
5
6
7 kb
(A)
n
5' UTR
ORF 1
ORF 2
3' UTR
DNA finger
homology
Noncoding
ORF
(A)
n
dA-rich
region
RT homology
Figure 1.8
Structure of a full-length human LINE (L1) element. UTR: Untranslated
region. ORF: Open reading frame. RT: Reverse transcriptase.
