Orangutans host ancient jumping genes

These tiny pieces of mobile DNA are able to copy themselves using a method similar to retroviruses. They can be thought of as molecular fossils, as a shared Alu element sequence and location within the genome indicates a common ancestor. But, because this is an inexact process, a segment of "host" DNA is duplicated at the Alu insertion sites and these footprints, known as target site duplications, can be used to identify Alu insertions.

"However, it has long been recognized that only a small fraction of these elements retain the ability to mobilize new copies as 'drivers,' while most are inactive," said Batzer, Boyd Professor and Dr. Mary Lou Applewhite Distinguished Professor of Biological Sciences. "In humans, telling the difference has proven quite difficult, mainly because the human genome is filled with plenty of relatively young Alu insertions, all with slight differences while at the same time lacking easily identifiable features characteristic for Alu propagation. This makes it hard to find their 'parent' or 'source Alu' from potentially hundreds of candidates that look similar."

In contrast to humans and other studied primates, recent activity of Alu elements in the orangutan has been very slow, with only a handful of recent events by comparison. This itself is very unique and was a highlighted feature of the Batzer Lab's previous Nature publication focusing on the Orangutan Genome.

"In the current study, we were able to discover the likely source Alu, or founder, of some of the very recent Alu insertions unique to the orangutan. This is significant for many reasons," said Walker. "First, this study represents only the second study that identified a driver Alu element. In addition, this driver is more than 16 million years old!"

Analysis of DNA sequences has found over a million Alu elements within each primate genome, many of which are species specific: 5,000 are unique to humans, while 2,300 others are exclusive to chimpanzees. In contrast, the orangutan lineage (Sumatran and Bornean orangutans) only has 250 specific Alu. Even though the Alu discovered in this study is old enough to be shared in human, chimpanzee, gorilla and orangutan genomes, its primary "jumping" has been in orangutans.

"Furthermore, this ancient 'backseat driver' created several daughter elements over the course of several millions years and a relatively young daughter element (found only in Sumatran orangutans and absent from Bornean orangutans) also appears to mobilize and has created offspring Alu copies of itself," said Konkel. This is promising new evidence that Alu propagation may be 'waking up' in orangutans.

The identification of an Alu element with the ability to mobilize itself contributes to the understanding of the evolution of Alu elements and their impact on primate genomes. Moreover, the features of this Alu element can be used to search for other source elements in different species including humans, which could lead to advances in our understanding of just how dynamic our genome really is.