The ABCs of RNA

Q: What is RNA?

A: RNA is one of the basic building blocks of a cell. It and DNA are similar in more than name alone: They are both chemicals made up of a series of four different nucleic acids, like four different colored beads on a string. The difference between the two is in their size and stability. DNA in most cells is hundreds of millions of beads long, consisting of two strands coiled around each other. RNA may contain thousands of nucleic acids in a single strand and tends to be short-lived. Another difference is location. The long-lasting DNA remains huddled in the cell's nucleus while the RNA flits around the cell.

Q: How do RNA and DNA interact?

A: The central dogma of genetics holds that double-stranded DNA makes single-stranded messenger RNA (or mRNA) that makes protein, which is the workhorse of the cell. The DNA is like a permanent encyclopedia of the cell's genes; the mRNA is like a transcribed note, fleetingly carrying protein-coding instructions from the nucleus.

Q: What did Fire, Mello and their colleagues describe in their 1998 Nature paper?

A: They did an elegant set of experiments showing that double-stranded RNA has the unusual ability to destroy an mRNA with a matching sequence of nucleic acids. By eliminating the mRNA, it halts the orderly process of DNA to mRNA and mRNA to protein. The process is now known as RNAi, or RNA interference.

Q: What led Fire and his colleagues to study RNAi?

A: Researchers studying plants had accumulated significant evidence that some forms of RNA might be suppressing the ability of an active gene to produce protein. In addition to the intriguing data in plants, some people studying roundworms had found that experimentally injected RNA, which they thought would lead to an increase in proteins encoded by that RNA, instead inhibited the production of those proteins. That was like getting hints that a neighbor had a secret life destroying her own landscaping. It warranted a closer look.

Q: How did they look closer?

A: Fire and his colleagues injected worms with a single strand of RNA—a strand that, according to the usual dogma, should up the production of a protein. That protein then diminished slightly. Injecting the reverse RNA strand had the same effect. Next they injected a double strand of that same RNA and wiped out production of the protein. The fact that a double-stranded RNA, which people didn't think normally existed, had any biological role shook up the research community. It turns out that the slight effect of the single-stranded RNA was due to some double-stranded contaminants.

Q: Does RNAi take place in all organisms?

A: Although RNAi was initially noticed in plants and then carefully described by Fire, Mello and their colleagues in worms, it quickly became apparent that RNAi works in all plants, animals and even lower organisms. It was a widespread phenomenon that had gone completely unnoticed.

Q: Even before Fire published his paper, were there known exceptions to the central dogma about RNA's role?

A: Yes. Some viruses carry their genetic code in RNA instead of DNA. When the virus inserts its RNA into a host cell, the RNA acts like a transcribed mRNA note and directs the cell to start making proteins. Some viruses use a single strand of RNA as their genetic encyclopedia, while others contain their genetic code in a double-stranded RNA.

Credit: Linda Cicero

Andrew Fire paced in his backyard early Monday morning as he fielded phone calls from the press regarding his research and reaction to winning the Nobel Prize.

Q: How does RNAi work?

A: It took may years of work by Fire and others to figure this out. First the double-stranded RNA teams up with an aptly named protein complex named Dicer, which chops the long RNA into short pieces. Then another protein group called RISC discards one of the two RNA strands. What's left is a RISC-docked, single-stranded RNA looking for a match. In a kind of molecular ambush, the RISC complex binds and destroys the mRNA with a matching sequence of nucleic acid beads.

Q: What normal cellular processes use RNAi?

A: RNAi appears to have two normal roles in the cell. The first is as a safeguard against viruses. If the only time a cell would normally encounter double-stranded RNA is during a viral attack, then it only makes sense that the cell would, over time, evolve ways of defending against that foreign body and the mRNA it creates. The second role for RNAi is in development. It turns out that, unbeknownst to researchers a decade ago, DNA does code for some double-stranded RNAs. Those dsRNAs are usually produced during development, where they stop the cell from producing a particular protein. This is one way for both plants and animals to regulate which proteins are being made as the organism develops new cells and tissues.

Q: How did Fire's discovery change the tools available to geneticists?

A: Until 1998 researchers had abundant tools for adding new genes to cells but no simple way to find out what would happen if they took a gene away. That left one side of genetic research more or less unexplored. RNAi filled that gap. It is an extremely effective way of scaling down how much protein is made by an active gene. That makes it a great tool for studying what a protein normally does in the cell, much like learning how a car works by dismantling it. Using RNAi, a researcher can remove a protein then monitor the results in the cell.

RNAi is also widely used to screen all the proteins in the cell one by one to find proteins of interest. That's like figuring out which car part is responsible for steering by removing each part and seeing which ones, when absent, eliminate the ability to steer. None of these experiments was possible before Fire and Mello sussed out RNA's double life. Now it's practically routine.

Q: Could RNAi be used for therapy?

A: Until RNAi came along, gene therapy was restricted to diseases such as hemophilia or cystic fibrosis, where a healthy copy of a gene could replace a mutated gene and cure the disease, at least in mice. RNAi opened up possible gene therapy for diseases caused by an overabundance of normal protein. RNAi could also be harnessed to block viral infections and to stop the overproduction of the protein that drives macular degeneration, the leading cause of blindness.

Q: Why should people care about RNAi?

A: Two reasons. First, one mission of science is to discover how the world works. The discovery of RNAi revealed a previously unknown mechanism within the cell. Second, although RNAi first came to light in plants and worms, it quickly became apparent that it also takes place in other animals, including humans. That means that this process could lead to novel treatments for disease.