282
Anthology of Human Repetitive DNA
captured by the nonautonomous trans-
posons (analogously to MuDR transposons
in the
Arabidopsis thaliana
genome).
The most abundant human hAT fami-
lies are
Charlie10, Charlie5, Cheshire
and
their nonautonomous companions repre-
sented by
60 000,
50 000 and
40 000
copies respectively (see Table 8). As in-
dicated above, there are no active DNA
transposons in the human genome. The
youngest hAT elements are
Charlie3
re-
peats that are
8% diverged from their
family consensus sequence. Given the
standard neutral mutation rate in the
human
genome,
this
corresponds
to
35 million years. Most of the human
hAT-like families are much older and they
might have been active in a common an-
cestor of primates and rodents.
3.3.2
Mariner/Tc1-like Transposons
The Mariner/Tc1 superfamily reflects the
names of the two founding DNA trans-
posons
mariner
and
Tc1
,F
r
s
td
i
s
c
o
v
-
ered in the
Drosophila melanogaster
and
Caenorhabditis elegans
genomes. Members
of this superfamily are characterized by
2-bp target site duplications (usually TA),
by
28-bp TIRs, and by the 5
0
-CA
...
TG-
3
0
termini. However, some elements may
have different termini; for example, HS-
MAR1 and HSMAR2 are characterized by
the 5
0
-TT
...
AA-3
0
and 5
0
-CG
...
CG-3
0
,re
-
spectively. Mariner/Tc1 transposases are
distantly related to a broad set of bacterial
transposases similar to that encoded by
IS630 insertion element, and are charac-
terizedbytheconservedDD
35
Emotif.
3.3.3
piggyBac-like Transposons
The piggyBac superfamily includes DNA
transposons with TTAA TSDs, the
15-
bp terminal inverted repeats, the 5
0
-CCC
and GGG-3
0
termini, and the unique
piggyBac transposase. The piggyBac trans-
poson was Frst discovered as an active
mobile element in the cabbage looper,
Trichoplusia ni
. The human transposon
called
Looper
was the Frst piggyBac-like
element identiFed outside cabbage looper.
It was reconstructed from copies trans-
posed
100 million years ago. Since then,
piggyBac-like elements were identiFed in
nonmammalian vertebrates, insects, and
Fshes. In addition to Looper, the human
genome harbors MER75 and MER85 trans-
posons that were active 10 to 50 million
years ago. Only
2000 copies of the
piggyBac-like elements are present in the
human genome.
3.3.4
MuDR-like Transposons
MuDR/Mu transposons, also known as
Mutators
, were Frst discovered in maize.
They are characterized by 9 to 10-bp TSDs
and by
70 to 400-bp TIRs, typically end-
ing with 5
0
-GGG and CCC-3
0
conserved
termini. However, some families of MuDR
transposons in the
A. thaliana
genome can
transpose without any discernible TIRs.
Different autonomous MuDR transposons
encode similar MuDR-like transposases,
which share common conserved mo-
tifs with bacterial IS256-like transposases.
Currently, only two families of MuDR-
like transposons are known to be harbored
by the human genome. One of them
is represented by the nonautonomous
transposons Ricksha and Ricksha
0, and
characterized by 9 to 10-bp TSDs,
70-bp
TIRs, and 5
0
-GGG and CCC-3
0
termini.
Ricksha and Ricksha
0we
reac
t
ive40to
100 million years ago and are present in
only
1000 copies in the human genome.
Ricksha is a composite transposon that
differs from Ricksha
0byhav
inga
700-
bp insertion of the HERVL endogenous
retrovirus including its long terminal re-
peat (MLT2B). Presumably, the HERVL
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