They used the RNAi process itself to find new genes that participate in the gene-silencing mechanism, which someday may help to fight human disease. The report will appear in the journal Science and is receiving early online release on the Science Express website.

"The gene activation produced by RNAi is exquisitely specific, which gives it enormous potential for therapeutic application," says Gary Ruvkun, PhD, of the MGH Department of Molecular Biology, the study's senior author. "Imagine short, double-stranded RNA molecules that could be synthesized quickly and inexpensively to silence a single gene. Promising targets could include viruses like HIV and hepatitis C or cancer-causing oncogenes. An RNAi-based treatment for age-related macular degeneration is already in clinical trials." Ruvkun is a professor of Genetics at Harvard Medical School.

RNAi was originally identified in the C. elegans roundworm and the flowering plant Arabidopsis thaliana, both of which are common model organisms for biological research. The process interrupts the usual transfer of instructions from double-stranded DNA, through single-stranded messenger RNA and finally into proteins. Short, double-stranded pieces of RNA bind to the complementary messenger RNA segments, shutting down gene expression. RNAi occurs naturally in plants and animals and may help control resistance to viral infection, among other functions.

For the current study, lead author John Kim, PhD, and his colleagues developed a strain of C. elegans into which they added a gene that caused the worms to glow under ultraviolet light but also turned that gene off using RNAi. They then used RNAi to inactivate every one of the worms' 19,000 genes by feeding the worms bacteria that produce double-stranded RNA for each gene. Inactivation of about 90 genes caused the worms to glow, indicating that those genes were essential to the RNAi process that had been suppressing expression of the fluorescence gene.

Some of the identified genes “ many of which have human counterparts “ code for proteins involved with the packaging and processing of RNA, but others may be involved with the regulation of DNA itself, including the repair of DNA damage. "These new steps indicate there is more to RNAi than RNA destruction," says Kim. "And the connection to DNA damage pathways, which was totally unexpected, suggests a potential connection between RNAi and the control of cell division in cancer."

The researchers note that better understanding the mechanisms underlying RNAi could help transform what has been a research tool into a powerful therapeutic tool. Although the process has worked well in studies of cultured human cells, it has not yet been effective for experimentally suppressing gene expression in living mammals. Identifying each step in the RNAi process could lead to more successful inactivation of disease-related genes. And in addition to the technique's potential for gene silencing, controlling levels of RNAi that may underlie some cancers or be used in viral replication may offer further clinical potential.

Along with Kim, the study's co-first authors are Harrison Gabel and Ravi Kamath, MD, PhD, of the MGH Department of Molecular Biology. Additional authors are Michael Dybbs and Joshua Kaplan, PhD, of MGH; Muneesh Tewari, MD, PhD, Jean-Francois Rual, Nicolas Bertin, and Marc Vidal, PhD, of Dana-Farber Cancer Institute; Amy Pasquinelli, PhD, of the University of California at San Diego; and Scott Kennedy, PhD, of the University of Wisconsin.

mgh.harvard/