This bias has implications for understanding and perhaps someday even preventing and treating genetic diseases. "For us to really understand how the genetic diseases occur, we need to know when the elements integrate -- at what point in human development this occurs," says Makova. "We are studying evolution mostly, but our results are relevant to genetic diseases caused by insertions of transposable elements in the genome. For instance, Alu insertions are known to cause some types of neurofibromatosis, hemophilia, breast cancer, Apert syndrome, cholinesterase deficiency, and complement deficiency."

When transposable elements were first discovered in the 1940s, many in the scientific community labeled them as "junk" DNA. Says Makova, "I don't think many people agree that they are 'junk' DNA any longer. Many of these elements have function. Alu elements frequently possess the regulatory elements. Both the Alu and L1 elements are often involved in recombination, the phenomenon under which the genome can undergo rearrangement and reshuffling."

Kvikstad and Makova spent a year analyzing the primate data. Previously, together with Francesca Chiaromonte, associate professor of statistics at Penn State, they had worked together on a project looking at primate insertions and deletions of a much smaller size, under 30 base pairs. "We are the first team to look into this much detail at the distribution of transposable elements on human sex chromosomes," Makova says.

Kvikstad points out other important implications of this study. "In particular, we noted that gene density was not a significant predictor of either Alu or L1 element density, at any evolutionary time point," she says. "By contrast, density of conserved non-coding DNA or 'most conserved elements' was a strong negative predictor of L1 density -- so L1 elements are scarce in regions of the genome that might contain many of these potentially functional noncoding DNAs. This is an important distinction, since previous studies inferring the action of natural selection in shaping the densities of transposable elements relied on gene density as a proxy for natural selection. Our results suggest that the potentially functional DNA residing in these most-conserved elements may be an additional hallmark of natural selection."

Source: Penn State