(Philadelphia, PA) - In experiments with transgenic
mice, University of Pennsylvania School of Medicine
researchers discovered the remaining steps in the complicated process
of how the largest class of jumping genes replicates and inserts
themselves within the human genome. Haig H. Kazazian, Jr.
MD, Chair of the Department of Genetics, and colleagues
at Penn published their findings in the February issue of Genome
Research. This knowledge may shed light on the origins of "junk"
DNA, parts of the genome for which no function has yet been discovered.
Jumping genes-also called mobile DNA or transposons-are sequences
of DNA that can move or jump to different areas of the genome within
the same cell. They are a rare cause of several genetic diseases,
such as hemophilia and Duchenne muscular dystrophy.
Retrotransposons are one class of jumping genes, with the L1 family
being the most abundant in the human genome. Retrotransposons move
by having their DNA sequence transcribed or copied to RNA, and then
instead of the genetic code being translated directly into a protein
sequence, the RNA is copied back to DNA by the retrotransposon’s
own enzyme called reverse transcriptase. This new DNA is then inserted
back into the genome. This process of copying is similar to that
of retroviruses, such as HIV, leading scientists to speculate about
a viral origin for retrotransposons.
“L1 retrotransposons, which are the only active mobile DNA
elements in humans, have accounted for about 30 percent of the human
genome by their own insertions and by driving the insertion of other
kinds of elements,” says Kazazian. “In fact, humans
have over 500,000 L1 retrotransposons within an individual genome.”
In order to learn about the effects of L1 retrotransposon insertions
into the human genome, the researchers made a transgenic mouse in
which human L1 retrotransposons could replicate. They injected several
copies of a human L1 retrotransposon to create the transgenic mouse.
In subsequent generations, the retrotransposons moved within the
offsprings’ genomes and each new insertion could be detected
by the investigators. The researchers characterized 51 new jumps
of L1, finding that insertions landed in random genomic regions.
Several L1 insertions included small pieces of extra DNA.
While tracing the origin of this extra DNA, Daria Babushok,
an MD/PhD student in the Kazazian lab, came up with the missing
steps in the mechanism of retrotransposon replication. “It
was known previously that the enzyme endonuclease cleaves one of
the strands of cellular DNA and then the retrotransposon inserts
by binding to that cleaved DNA strand and copying itself onto that
strand,” she says. “It sneaks in there.”
How the retrotransposon finally integrated and pasted itself back
together was unknown, until this paper. “What we saw in our
insertions hinted at the possibility that reverse transcriptase
actually jumps onto the second DNA strand and continues the synthesis,”
she explains. “We think that this is how the second part of
the element integrates into the genome. If this mechanism proves
to be correct, it will bring us much closer to knowing how more
than half a million retrotransposons have accumulated in the human
Eventually, continuous jumping by retrotransposons expands the size
of the human genome and may cause shuffling of genome content. For
example, when retrotransposons jump, they may take portions of nearby
gene sequences with them, inserting these where they land, and thereby
allowing for the creation of new genes. Even otherwise unremarkable
insertions of L1 may cause significant effects on nearby genes,
such as lowering their expression.
Now, by knowing the final steps in retrotransposon replication and
being able to follow and map new insertions in animals, the researchers
will be able to more fully understand how L1 retrotransposons are
able to invade the human genome.
“We were able to obtain a snapshot of a large number of new
L1 jumps in a situation closely mimicking what occurs every day
in the human genome,” says Babushok. “Importantly, occasional
small additions of extra DNA sequences at the ends of new L1 insertions
gave us tantalizing leads to the L1 retrotransposon replication
mechanism. We are very excited to follow this thread to confirm
our proposed mechanism and to come closer to a complete understanding
of the interaction between L1 retrotransposons and our genomes.”
The research was supported by grants from the National Institutes
of Health. Study co-authors are Eric M. Ostertag, Christine E. Courtney,
and Janice M. Choi, all from Penn.
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