Turning off rice genes

University of Delaware researchers, in collaboration with U.S. and international colleagues, have found a new type of molecule - kind of 'micro-switch' - that can turn off genes in rice, which is the primary source of food for more than half the world's population.
Composed of short lengths of ribonucleic acids (RNAs), on the order of about 20 nucleotides long, these novel molecules, called natural antisense microRNAs (nat-miRNAs), target the genes sitting directly across from them on the opposite strand of DNA in a rice cell.
In addition to uncovering a new genetic switch and gaining insight about its pathways and evolution, which are important to the health of a grain that feeds most of the world, the research also may help scientists locate this type of novel gene regulator in other organisms, including humans. MicroRNAs regulate 30 percent of human genes and thus are critical to human health and development.
MicroRNAs are small RNA molecules that play a key role in regulating cellular processes, including a cell's development and its responses to stress. These micro-molecules bind to specific messenger RNA molecules, which carry instructions to the cells to make particular proteins. This binding typically causes the messenger RNAs to be degraded in plant cells.
Some 240 microRNAs previously had been annotated in rice. Using a high-throughput gene-sequencing technique, Massively Parallel Signature Sequencing (MPSS), the UD research team analysed over 4 million small RNAs from six rice samples, which yielded 24 new microRNAs, including the unique new group of molecules called natural antisense microRNAs.
When a gene is ready to produce a protein, its two strands of DNA unravel. The first strand, called the ‘sense’ transcript, produces messenger RNA, which carries the recipe for making a specific protein. However, the other strand of DNA may produce a complementary antisense RNA molecule, which sometimes can block production of the protein, thus turning off, or ‘silencing’, the gene.
In the newly discovered case, the sense messenger RNA and antisense RNA operate differently, and different pieces are spliced out of each. These splicing differences limit the pairing ability between the sense and the antisense to a small region that includes the microRNA. In addition, splicing of the precursor of natural antisense microRNAs allows a hairpin to form, and hairpins are a requirement for any microRNA to be made.
Such microRNAs are not present in the common research plant Arabidopsis, which is a dicotyledon, a plant group that has two seed leaves (cotyledons) when it first sprouts. However, the UD team has identified the novel microRNAs in monocotyledons such as rice, corn and other grains.
The next step in the research will be to try to understand how microRNAs help rice plants respond to adverse environmental conditions, such as drought or limited nutrient availability.
In addition, the UD group currently is analysing small RNAs in a diverse set of plant species to determine if this new class of microRNA may be present in a broader set of monocots or other plants.
The discovery is reported in the March 25 issue of the Proceedings of the National Academy of Sciences of the United States of America.