262
Anthology of Human Repetitive DNA
Master gene
Transpositions
Mutations
Alignment
Consensus sequence
(Reconstructed master gene)
Fig. 2
Molecular paleontology of transposable elements. The top
white rectangle represents an ancient active transposon that
multiplied into interspersed repeats shown as gray rectangles
subsequently marked by black vertical bars indicating mutations.
Most of these mutations can be ‘‘undone’’ after multiple
alignments and construction of a consensus sequence
representing the reconstructed transposon (bottom white
rectangle). The gray bar in the consensus sequence indicates an
unresolved mutation.
groups. Two of these groups belong to
a class of retroelements that include
non-LTR retrotransposons and endoge-
nous retrovirus-like elements also known
as
long terminal repeat
(LTR) retrotrans-
posons. Retroelements proliferate via re-
verse transcription of their RNA expressed
in the host cell. An RNA copy of the
transcribed retroelement is used as a
template to produce its DNA copy, the
so-called cDNA, which can be inserted
in the genome. In non-LTR retrotrans-
posons, a nick in the host DNA primes
cDNA formation, whereas in retroviral-
like elements, the DNA nicking and cDNA
integration occur after reverse transcrip-
tion. The nicking and cDNA formation are
catalyzed by the endonuclease/integrase
(IN) and reverse transcriptase (RT), re-
spectively, encoded by the transposable
element
itself
or
by
one
of
its
au-
tonomous relatives present in the genome.
Unlike DNA transposons, active retroele-
ments do not relocate from their original
position.
The third group of TEs is represented by
the
cut-and-paste
DNA transposons, called
so because they are excised (cut) from
the original genomic location and inserted
(pasted) into a new site. Typically, a
single enzyme called
transposase
mediates
the process.
All groups of TEs are composed of
autonomous and nonautonomous ele-
ments. An autonomous element encodes
a complete set of enzymes characteristic
of its family. Nonautonomous families
use the protein machinery of their au-
tonomous relatives. Therefore, the nonau-
tonomous TEs can be viewed as para-
sites competing for enzymes encoded by
the autonomous elements. Both groups
also require additional cellular factors for
ampliFcation.
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