280
Anthology of Human Repetitive DNA
basic properties of human DNA trans-
posons were deduced from sequence anal-
ysis of human repetitive DNA, followed
by reconstruction of DNA and protein se-
quences encoded by once-active elements.
On the basis of their structural common-
alties, eukaryotic DNA transposons can be
divided into eight different superfamilies,
of which six are represented in the hu-
man genome (Table 7). DNA transposons
that belong to the same superfamily, even
those from different vertebrates, plants,
and insects, are characterized by common
structural hallmarks such as similar TIRs,
transposases, and the same characteris-
tic sizes of TSDs. Additional superfamily
characteristics include conserved termini
of TIRs, usually 2 to 3 bp long. Like
other classes of TEs, DNA transposons are
represented by autonomous and nonau-
tonomous elements.
The human genome harbors families
derived from over 29 autonomous trans-
posons. Of these, over 25 belong to the hAT
and
mariner/Tc1
superfamilies (Table 8).
However, only 13 of them have been recon-
structed and characterized in more detail.
Some of the most abundant families of
nonautonomous hAT elements, such as
MER5A and Cheshire
A, are represented
by more than 10
4
copies each. Overall,
the transposon-derived interspersed re-
peats account for
5% of the human
genomic DNA.
3.3.1
hAT-like Transposons
The superfamily of hAT-like elements was
named after the initials of
hobo, Activator
and
Tam
transposons identiFed in the fruit
fly and maize. They are flanked by
15-
bp terminal inverted repeats that include
characteristic 5
0
-CA and TG-3
0
termini, and
generate 8-bp target site duplications upon
integration in the genome. Autonomous
hAT-like transposons are
3000-bp long
and encode
500-aa transposase similar
to transposases encoded by all known
hAT-like transposons detected in different
eukaryotic species. Analogously, the OR±s
in the human hAT-like transposons are
also expected to encode the transposases.
The
most
abundant
hAT
elements
are the nonautonomous deletion prod-
ucts of the corresponding autonomous
transposons. They retain TIRs, but the
Tab. 7
Superfamilies of cut-and-paste DNA transposons represented in
humans.
Superfamily
Related bacterial
transposases
Termini
TSDs
Mariner/Tc1
IS630
CA-TG
2 (TA)
hAT
CA-TG
8
piggyBac
CCC-GGG
4 (TTAA)
MuDr
a
IS256
GGG-CCC
9–10
Harbinger
b
IS5
GGG-CCC
3
P
c
CA-TG
7–8
a
Only nonautonomous
Ricksha
has
MuDr
hallmarks: 9-bp TSDs, 70-bp
TIR, 5
0
-GGG and CCC
0
-3
0
termini.
b
Harbinger
-and
c
P
– like transposases are present as single-copy genes conserved in
mammals including humans.
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