In a second paper in the same issue of Nature, M.D./Ph.D. candidate Jeffrey Han and Boeke report that the human jumping gene is relatively lethargic because its instructions are hard for cells to read. By replacing some of the gene’s instructions with alternatives cells prefer, the researchers made the first highly active, artificial jumping gene that is potentially efficient enough to use in mice.

By inserting the artificial jumping gene into cells of a mouse embryo, scientists should be able to develop mice in which random genes are either silenced completely or simply “quieted” by the jumping gene’s intrusion. Studying these mice should reveal the function and identity of the disrupted gene — in that order.

“The ability to study genetics “backward” — to disrupt a random gene, determine its role in the animal and then identify it — has been crucial in understanding genes in fruit flies and yeast, and now we should be able to do it fairly efficiently in mice,” says Boeke, whose lab is already starting to develop the necessary technology.

Based on his research, Boeke suggests that the genes’ DNA is much more than just “junk” in our genome. Instead, he proposes that, long ago, jumping genes’ multiple insertions likely played a major role in establishing the evolutionary shifts that now distinguish mice from men, and that even now their DNA affects how other genes are used.

Both mice and men share jumping genes known as L1 retrotransposons, some of which are “young” and still active, but most of which are “rusting hulks” that account for more than 30 percent of our respective DNA. But even the “young” ones aren’t active enough to efficiently introduce genetic changes in mice that can be passed from generation to generation.

The reason, the researchers report, is that the human jumping gene’s instructions consist of too much of one DNA building block, and not enough of the three others, an imbalance that bogs down the cell’s machinery as it tries to transcribe the DNA into RNA. Instead of plodding through, the machinery just gives up.

To “improve” these genetic instructions, Han took advantage of the fact that multiple sets of three DNA building blocks call for the same protein building block, or amino acid. By swapping most of the gene’s original DNA “triplets” with alternatives the cell prefers, Han balanced the gene’s building blocks without changing its protein-making instructions. The researchers have filed a provisional patent on the artificial gene.

Han found that mammalian cells readily used the artificial gene, translating its genetic information into RNA and then into the proteins that help the gene jump. In a standard test of jumping genes’ activity, the artificial gene jumped upwards of 200 times more often than natural jumping genes.

The discoveries have led the researchers to propose a new way retrotransposons could contribute to evolutionary changes and to disease, besides disrupting a gene entirely. The researchers’ bottom line: The prevalence of hard-to-read jumping gene DNA inside a gene may subtly alter the extent to which it is used by the cell.

“Roughly 70 percent of human genes contain some bit of the natural jumping gene’s DNA, and big genes have multiple scraps or even complete retrotransposons,” says Boeke. “These bits quite likely reduce the amount of RNA made from these genes, and in some cases even change the gene’s message and alter the gene’s protein-encoding regions.”

To test their model’s likelihood, postdoctoral fellow Suzanne Szak, Ph.D., surveyed thousands of the most- and least-used human genes. Genes containing more of the jumping gene’s hard-to-read DNA were used substantially less than those with shorter and fewer jumping gene bits, she found.

“The presence of jumping gene DNA in genes represents little experiments in the genome — if the changes benefit or don’t harm the cell or the person, they continue to be passed on from cell to cell or generation to generation,” adds Boeke. “If not, they would gradually fade from the genome.”

The studies were funded by the National Cancer Institute and the Medical Scientist Training Program at Johns Hopkins. Authors on the artificial jumping gene paper are Han and Boeke. Authors reporting the jumping gene’s hard-to-read DNA are Han, Szak and Boeke. Szak is now at Biogen Inc.