Want to expand a genome? Previous thinking suggests you only need some transposable elements, often nicknamed “jumping genes”, to repeatedly, and irreversibly, insert into the genome. Time will take care of the rest.
However, new research is now challenging this view by revealing that transposable elements can also be deleted during evolution.
The new findings were recently reported by Louie van de Lagemaat, Dixie Mager and their colleagues from the Terry Fox Laboratory in Vancouver, BC. They compared the human, chimpanzee and Rhesus monkey genomes and found 37 instances where transposable elements were present in the primitive Rhesus monkey, but lost in the human and chimpanzee genome.
In finding that transposable elements can be deleted during evolution, van de Lagemaat and colleagues also discovered that such deletions occur between short flanking repeats of DNA — a finding that points to a mechanism for how genome size my be attenuated during evolution.
“Our work strongly suggests an important role for short, non-adjacent, identical segments of DNA in genomic deletions,” said Dr. Mager in a press statement, “and it lends insight into deletion mechanisms that help to counterbalance genome expansion in primates.”
Transposable elements are a well known cause of genomic expansion, and in mammals, have been reported to comprise upwards of 50% of the genome. The prevailing theory is that such expansions are unidirectional, with transposable elements becoming irreversibly maintained in a population over time.
However, this theory wasn’t what van de Lagemaat and colleagues were originally interested in. Instead, they were simply looking for new transposable elements in the human genome.
“We were looking at supposedly new transposable elements but they instead appeared to be of a very old variety,” said van de Lagemaat, who is the lead author of the current study. “So we started to wonder if some of them were deleted,” he said, thereby making them look new when they weren’t.
van de Lagemaat and colleagues therefore went about aligning the entire human, chimpanzee and Rhesus monkey genomes, to see how many transposable elements had deletions. They estimate that 0.5 to 1.0% of transposable elements that look like insertions are instead deletions. The results of the study appear in the September issue of Genome Research.
“The baseline belief is that anything can happen but some things are more frequent than others,” said van de Lagemaat about what he first thought when he saw the data. “This is one of those ‘any-things’ that isn’t very frequent,” he said.
Although the frequency of precise transposable element deletion is rare, van de Lagemaat said the mechanism that causes their deletion is not.
The mechanism involves flanking identical repeats of at least 10 base pairs of DNA, which play a role in recombining and removing DNA sequence between them. van de Lagemaat and colleagues suggest that 19% of genomic deletions between 200-500 base pairs since humans diverged from chimpanzees are due to these repeats.
“We are looking at a generalized deletion mechanism,” said van de Lagemaat, “and such deletions are important in a lot of circumstances like disease, giving us the potential to more deeply understand them.”