Anthology of Human Repetitive DNA
265
synthesis of the second strand, ligation,
and elimination of the L1 RNA, are
probably mediated by host enzymes.
The majority of L1 elements undergo
5
0
truncations
and
inversions
during
retroposition and, as a result, they are
represented mostly by 3
0
terminal portions
that are shorter than 1 kb in length.
Possible reasons for the truncation may
be digestion of the L1 RNA by cellular
ribonucleases, or premature termination
of the reverse transcription, or both.
Occasionally, transcription of L1 ele-
ments does not stop at the L1 polyadeny-
lation signal but continues until another
transcription termination signal encoded
by the host DNA is encountered. As a re-
sult, host sequences adjacent to the 3
0
L1
terminus and the new polyA sites may
be transduced by the L1 to a new ge-
nomic location. Over 10% of the analyzed
L1 insertions in the human genome con-
tain 3
0
transduced sequences that range
from 30 bp to several kb in length. This
represents an attractive mechanism that
could be involved in exon shuffling in
the host genome. However, no real exons
have yet been detected in L1-transduced
sequences. Therefore, it is possible that
the L1-mediated 3
0
transduction is sup-
pressed in the vicinity of human genes.
Some L1 retrotransposons can also be
accidentally transcribed from upstream
promoters leading to transduction of ge-
nomic DNA flanking the 5
0
ends of L1
elements. Also, new L1 subfamilies can be
generated by the addition of both 5
0
and 3
0
flanking DNA.
3.1.2
L1-dependent Nonautonomous
Non-LTR Retrotransposons
There
are
two
major
groups
of
L1-
dependent non-LTR retrotransposons pre-
sent in the human genome: processed
pseudogenes, and SINEs that include Alu
and SVA elements. Elements from both
groups are flanked by
15-bp TSDs, have
the 3
0
polyA tails, and are inserted pref-
erentially into the TTAAAA target sites. It
has also been demonstrated experimen-
tally that the propagation of processed
pseudogenes and Alu elements is me-
diated by the L1-encoded RT. Therefore,
both processed pseudogenes and Alu re-
peats are classiFed as nonautonomous
non-LTR retroelements mobilized by the
L1 retroposition machinery. The L1 reverse
transcriptase, in a cis-acting manner, pref-
erentially binds the same mRNA molecule
it was translated from. Therefore, Alu and
other nonautonomous retropseudogenes
probably intercept the L1 RT while inter-
acting with ribosomal components.
3.1.2.1
Processed pseudogenes
Proces-
sed pseudogenes, or retropseudogenes, are
products of occasional retrotransposition
of spliced mRNA formed during regular
transcription of the host genes (±ig. 5).
Since transcription of these genes is usu-
ally driven by external pol II promoters,
processed pseudogenes do not include
the promoters. Therefore, it is extremely
unlikely that they can be repeatedly tran-
scribed and retrotransposed. Nevertheless,
the human genome is estimated to contain
at least 30 000 retropseudogenes formed
from a variety of host genes. The most
abundant retropseudogenes appear to be
derived from highly expressed genes rang-
ing from those coding for small nuclear,
nucleolar, and cytoplasmic RNA, to those
coding for ribosomal proteins.
3.1.2.2
Alu repeats
Alu elements were
Frst discovered using DNA renatura-
tion–reassociation experiments that were
performed during the early era of repeat
studies. They are represented by more
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