University of Georgia 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."
The research is published in the Jan. 9 edition of the journal Nature.
In collaboration with researchers from Cornell, Washington University and Japan, geneticist Susan Wessler 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 percent of the rice genome comprises repetitive DNA that does not code for proteins and thus has no obvious function for the plant. 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 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. Recognizing 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 thus 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.
Building a brain, cell by cell: Researchers make a mini neuron network (of two)
23.05.2018 | Institute of Industrial Science, The University of Tokyo
Research reveals how order first appears in liquid crystals
23.05.2018 | Brown University
At the LASYS 2018, from June 5th to 7th, the Laser Zentrum Hannover e.V. (LZH) will be showcasing processes for the laser material processing of tomorrow in hall 4 at stand 4E75. With blown bomb shells the LZH will present first results of a research project on civil security.
At this year's LASYS, the LZH will exhibit light-based processes such as cutting, welding, ablation and structuring as well as additive manufacturing for...
There are videos on the internet that can make one marvel at technology. For example, a smartphone is casually bent around the arm or a thin-film display is rolled in all directions and with almost every diameter. From the user's point of view, this looks fantastic. From a professional point of view, however, the question arises: Is that already possible?
At Display Week 2018, scientists from the Fraunhofer Institute for Applied Polymer Research IAP will be demonstrating today’s technological possibilities and...
So-called quantum many-body scars allow quantum systems to stay out of equilibrium much longer, explaining experiment | Study published in Nature Physics
Recently, researchers from Harvard and MIT succeeded in trapping a record 53 atoms and individually controlling their quantum state, realizing what is called a...
The historic first detection of gravitational waves from colliding black holes far outside our galaxy opened a new window to understanding the universe. A...
A team led by Austrian experimental physicist Rainer Blatt has succeeded in characterizing the quantum entanglement of two spatially separated atoms by observing their light emission. This fundamental demonstration could lead to the development of highly sensitive optical gradiometers for the precise measurement of the gravitational field or the earth's magnetic field.
The age of quantum technology has long been heralded. Decades of research into the quantum world have led to the development of methods that make it possible...
02.05.2018 | Event News
13.04.2018 | Event News
12.04.2018 | Event News
23.05.2018 | Life Sciences
23.05.2018 | Life Sciences
23.05.2018 | Physics and Astronomy