Jumping genes caught
A team at Johns Hopkins University has revealed 1.016 new insertions of RIPs or retrotransposon insertion polymorphisms, thereby expanding the catalog of insertions that are present in some individuals and absent in others.
The scientists used bioinformatics to compare the standard assembly of genetic elements as outlined in the reference human genome to raw whole-genome data from 310 individuals made available by the 1000 Genomes Project.
Retrotransposons are travelling bits of DNA that replicate by copying and pasting themselves at new locations in the genome. Having duplicated themselves and accumulated over evolutionary history, transposable elements now make up about half of the human genome.
"In any individual, only between 80 to 100 retrotransposons are actively copying and inserting into new sites," said lead scientist Haig Kazazian.
"We`re not only discovering where they are and who has which ones, but also finding out that they insert with a remarkable frequency — on the order of one in every 50 individuals has a brand-new insertion that wasn`t in their parents," he added. The researchers recognized L1 retrotransposons –distinguishing them from the vast amount of fixed "fossil" transposable elements that litter the genome — because these actively jumping genes are human specific and almost exactly the same in sequence from one person to another.
"Our genome contains around half a million interspersed L1 sequences that have accumulated over evolutionary history, along with over a million more repeats, most of which were mobilized by L1 elements," said team member Adam D Ewing.
"Since the vast majority of these are ancestral and therefore common to all humans and even some of our primate relatives, we can ignore them and focus on L1s that contain human-specific characters in their sequences. Those are the actively mobilized elements responsible for considerable genomic diversity among human individuals," he added.
The findings have been published in the `Genome Research` journal.