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.
Organ Crosstalk: Fatty Liver Can Cause Damage to Other Organs
18.08.2017 | Deutsches Zentrum für Diabetesforschung
Modern genetic sequencing tools give clearer picture of how corals are related
17.08.2017 | University of Washington
Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.
As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...
Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.
Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...
For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.
While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...
An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.
The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...
A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.
Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...
16.08.2017 | Event News
04.08.2017 | Event News
26.07.2017 | Event News
18.08.2017 | Life Sciences
17.08.2017 | Physics and Astronomy
17.08.2017 | Earth Sciences