Ping or pong - understanding the rice genome

Researchers studying rice genomes under a National Science Foundation Plant Genome Research Program award have identified the species' first active DNA transposons, or "jumping genes."

In collaboration with researchers from Cornell, Washington University and Japan, geneticist Susan Wessler from the University of Georgia also discovered the first active "miniature inverted-repeat transposable element," or "MITE," of any organism.

Rice (Oryza sativa), an important food crop worldwide, has the smallest genome size of all cereals at 430 million base pairs of DNA. About 40 per cent of the rice genome is comprised of repetitive DNA that does not code for proteins and, according to researchers, has no obvious function for the plant.

The scientists write that much of this repetitive sequence appears to be transposons similar to MITEs. But like most genomes studied to date, including the human genome, the function of this highly repeated so-called "junk DNA" has been a mystery.

The researchers maintain that the discovery of active transposons in rice provides startling new insights into how genomes change and what role transposons may play in the process.

Active DNA transposons can move new copies of DNA to different places in the genome. To hunt for active DNA transposons, the researchers made use of the publicly available genome sequences for two subspecies of rice, japonica and indica. The researchers reasoned that in plants where such transposons move actively there would be multiple copies of an almost identical sequence. If they could find the conserved sequences in the two rice genomes, then they could test for transposon movement in cell cultures because the number of elements should have increased over time.

Using this approach, the researchers found a repeated sequence of 430 base pairs that was identified as a candidate for an active MITE because of the high degree of sequence conservation among the copies. Recognising that it shared common size and other characteristics with MITEs, they named it "mPing" for "miniature Ping." They calculated that the entire genome of japonica rice contained about 70 copies of mPing, while indica rice had about 14 copies. When they looked in indica rice cell cultures, the number of mPing elements increased, suggesting that it was indeed actively transposing.

It was puzzling to understand how mPing could transpose, since MITEs do not code for any proteins and are consequently unable to move on their own. The researchers reasoned that there must be another "autonomous" transposon that encodes proteins, enabling itself and other related elements to move. To find this autonomous element, the researchers compared the mPing sequence with the japonica and indica rice genome sequences to look for longer, related elements.

They found two candidates: a long version called the "Ping" sequence and another shorter sequence they named "Pong." Ping lacked functional coding sequence and was also found only in japonica rice as a single copy. On the other hand, Pong was present in high copy numbers in all varieties, contained appropriate coding sequences, and also increased in number along with mPing during cell culture. This led the researchers to suspect that Pong, not Ping, is the autonomous element that causes mPing to transpose. It is also possible, the researchers speculate, that Ping and Pong may co-activate mPing in some cases.

Wessler and her collaborators have shed new light on the idea that transposons may be instrumental in promoting the diversity of plants during domestication. Their work meshes with an idea, raised almost 20 years ago by Nobel Prize-winning maize geneticist Barbara McClintock, that transposons are part of the dynamic forces shaping plant genomes.

The research findings will help researchers unravel the events leading to the origin, spread, and disappearance of miniature transposons. Remarkably, MITEs make up a large part of the non-coding DNA in plant genomes. Through studies of transposons such as MITEs, researchers will begin to understand the impact of so-called "junk DNA" on the dynamic structure and function of the genomes of all organisms.

Full findings are published in the 9 January edition of the journal Nature.