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. Recognizin
Contact: Manny Van Pelt
National Science Foundation