Every DNA segment in a eukaryotic genome normally replicates once and only once per
cell cycle to maintain genome stability. We show here that this restriction can be
bypassed through alternative transposition, a transposition reaction that utilizes
the termini of two separate, nearby transposable elements (TEs). Our results suggest
that alternative transposition during S phase can induce re-replication of the TEs
and their flanking sequences. The DNA re-replication can spontaneously abort to
generate double-strand breaks, which can be repaired to generate Composite Insertions
composed of transposon termini flanking segmental duplications of various lengths.
These results show how alternative transposition coupled with DNA replication and
repair can significantly alter genome structure and may have contributed to rapid
genome evolution in maize and possibly other eukaryotes.
To make accurate copies of its genome, a cell takes precautions to make sure each
section of DNA is only duplicated once in every round of copying. However, there are
some sections of DNA called transposons that can avoid these restrictions and be
duplicated more often.
Transposons are mobile pieces of DNA: they can be ‘cut’ from one
section of the genome and are able to ‘paste’ back in somewhere else.
The amount of mobile DNA in a genome varies a great deal between species, and in the
crop plant maize, it makes up nearly 85% of the genome.
Some transposons can move while the genome is being duplicated. If a transposon is
cut out of a section of DNA that has already been copied and is pasted into a site
that is yet to be copied, the transposon can be copied again. The transposon may now
be present in two different places in the genome.
If two transposons are close together on a section of DNA, both transposons can move
at the same time. As they move, they can carry along pieces of the genome,
transferring them from one site to another. These transferred pieces can include
sections of, or even entire, genes. This is called alternative transposition, but it
is not clear whether this process can happen when the genome is actively being
Here, Zhang et al. studied transposons in maize. The experiments found that
alternative transposition can take place between a site that has already been copied
and another site that is still waiting to be copied. Therefore, after the round of
copying is completed, both transposons and the flanking DNA can be present in two
places in the genome.
When single transposons move, or alternative transposition takes place, sections of
the genome can be rearranged and genes can be deleted or new ones can be created.
Therefore, transposons may have contributed to rapid evolution in maize and possibly