It is not every day that scientists reveal nature's best secrets, the ones that promise to deepen understanding of the biology of living things. The discovery of gene silencing by RNA interference (RNAi) is this kind of breakthrough. Researchers are using RNAi to reveal the function of genes in animals, plants, and humans. RNAi also offers a promising new approach to treating AIDS and a host of other diseases. Underscoring the importance of RNAi, Science magazine declared advances in this field to be the top scientific achievement of 2002.
Although scientists only discovered the existence of RNAi within the last decade, they now know that organisms have been using the process for millions of years. Researchers believe that RNAi's natural role is to tune the activity of genes, reducing their expression for purposes of growth and/or self-defense. When viruses infect cells, for example, they command their infected host to produce specialized RNAs to enhance viral survival. Researchers believe that RNAi is an ancient mechanism used to wipe away such unwanted, extra RNA, and some scientists speculate that it may even play a role in our immunity.
RNAi's use as a research tool began with an experiment gone wrong. Scientists studying the genetics of plant growth noticed a curious result. The researchers were attempting to deliver an extra "purple" gene to petunias, but the flowers instead bloomed stark white. The result evaded genetic logic and fascinated biomedical researchers, who yearned to understand how adding genetic material could somehow silence an inherited trait.
The mystery remained until, a few years later, two NIGMS-supported geneticists identified a similar process in animals. RNAi, they learned, operates like a molecular "mute button" to quiet individual genes. The two researchers, Andrew Fire, Ph.D., of the Carnegie Institution of Washington in Baltimore and Craig Mello, Ph.D., of the University of Massachusetts Medical School in Worcester, had been using a molecular tool called antisense RNA to dampen gene activity in roundworms and tease apart genetic factors that contribute to cell growth and tissue formation. In this technique, researchers cause the normally single-stranded RNA to bind to an opposite, or "anti-," strand. This blocks the RNA from delivering the instructions to make a protein.
To their surprise, Fire and Mello discovered that the activity of their laboratory preparation did not depend on the antisense RNA itself, but instead on a contaminant that was produced during the synthesis of the antisense RNA. The contaminant, it turns out, was a molecule of double-stranded RNA. Fire and Mello quickly learned that they could mute specific genes simply by feeding their experimental worms double-stranded RNA with the same sequence as the gene they wished to target.
RNAi took the research world by storm. NIGMS grantee Gregory Hannon, Ph.D., of Cold Spring Harbor Laboratory on Long Island, New York, dropped everything he was doing when he learned that RNAi could be used as a tool in fruit flies as well as worms. Using this popular insect model system, Hannon has uncovered a link between RNAi and Fragile X syndrome, which is the most common inherited form of mental retardation. Also at Cold Spring Harbor Laboratory, NIGMS grantee Shiv Grewal, Ph.D., led a team that discovered RNAi's pivotal role in the normal functioning of yeast cells, which share many features with the cells of humans. Grewal, who is now at the National Cancer Institute, has learned that the molecules that normally carry out RNAi help to organize chromosomes so they can be pulled apart during cell division, one of the most basic steps in the lives of all cells.
Basic scientists investigating gene function began to try RNAi in other organisms and found that the technique could be applied nearly universally to manipulate gene activity in many different model systems. However, researchers had sporadic and unpredictable success getting RNAi to work in cells from mammals. In 1999, the situation brightened when Hannon's group and a team of NIGMS-supported scientists from the Whitehead Institute for Biomedical Research in Cambridge, Massachusettsincluding David Bartel, Ph.D., Phillip Sharp, Ph.D., Thomas Tuschl, Ph.D., and Phillip Zamore, Ph.D.developed systems for conducting RNAi experiments in a test tube. Collectively, these approaches revealed RNAi's molecular modus operandi and led the way toward getting the technique to work in mammalian cells. The researchers learned that in RNAi, the double-stranded RNA is first chewed up into smaller RNA pieces by a newly discovered enzyme named Dicer. The scientists realized that RNAi silences gene activity through the action of these tiny RNA snippets, which they dubbed short interfering RNAs (siRNAs).
RNAi to the Rescue
Researchers predict that in addition to RNAi's potential for solving many of the mysteries encoded in our genes, the technique holds promise for new therapies. NIGMS grantee Yang Shi, Ph.D., of Harvard Medical School in Boston, Massachusetts, is one of several researchers who have crafted clever tools for getting living cells to produce specific siRNAs. These methods have greatly enhanced researchers' ability to explore RNAi's medical promise in mammalian cells. For example, in recent lab tests with isolated cells, Sharp and others have succeeded in using RNAi to kill HIV, the virus that causes AIDS. Biologists are now working hard on the very challenging problem of developing ways to deliver siRNAs to the body in order to make a practical means for treating, and perhaps preventing, disease.