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CELL BIOLOGY
RNA Puts on the RITS, Hushes DNASmall Interfering RNAs Lead RITS Complex in Forming Heterochromatin that Cloaks DNAEven in its own private boudoir, the nucleus of a cell, DNA is rarely naked. From head to toe, the double helix wears an intricately woven drapery of proteins. Some of the looser protein garments allow easy access to genes.
Steps toward gene silencing. Danesh Moazed (below left), Andre Verdel, and their collaborators demonstrate how small interfering RNA machinery in the cell muffles genes at the centromeres. As others have shown, an enzyme named dicer cuts double-stranded RNA into small interfering RNAs. In their new paper, the researchers report that small RNAs guide a newly identified protein complex, RITS, to a specific spot on the genome. The small RNAs exactly match the centromere sequence and may bind directly to the DNA, as shown above, holding the complex in place while other proteins join and help build the gene-silencing heterochromatin structure. (Image by Jeff Cleary; Photo by Leah Gourley)
But about half of the genome--including the centromeres at the cinched-in chromosome waists--travels through generations of cell division as tightly laced up as a proper Victorian woman. Known as heterochromatin, the tightly compressed DNA structure is locked down and guarded by specialized proteins to keep it from factors that normally would turn on the genes. The designer of this compact assemblage turns out to be the versatile regulatory mechanism RNA interference (RNAi). Working in fission yeast, Danesh Moazed, HMS associate professor of cell biology, and his collaborators identified the protein complex that uses small interfering RNAs to guide it to the region of the genome slated for silencing. They report their findings in the Jan. 30 Science. Regulatory RNA"RNA interference seems to be a pathway that touches every aspect of gene expression from transcription to messenger RNA degradation to translation," Moazed said. "It's an amazing regulatory mechanism. Small interfering RNAs can regulate single genes as well as a whole family of genes."
Now, there is direct evidence that small RNAs can act upon DNA through a protein complex. In the same issue of Science, a related paper from another collaborative group reports the first evidence of RNAi machinery promoting silent heterochromatic regions in the centromeres of a multicellular organism--in this case, fruit flies. The RNA interference pathway "was once thought to operate solely at a posttranscriptional level in the cytoplasm," according to Sarah Elgin of Washington University and James Birchler of the University of Missouri, the senior authors of the fruit fly paper. "The combined results suggest similarities in the way that heterochromatin is formed in both groups of organisms." For the fission yeast paper, Moazed's group teamed up with the lab of geneticist Shiv Grewal, now a senior investigator at the National Cancer Institute. Two years ago, Science named small interfering RNAs as the number one breakthrough of the year, and they stayed on the magazine's top-10 list of advances last year. In one of the highlighted discoveries, Grewal and his colleagues had shown that small RNAs have a role in organizing the genome and modifying chromatin. In the new paper, the Moazed and Grewal labs show the mechanism behind the action. The Blazed PathwayThe project started when first author Andre Verdel, a postdoctoral fellow in Moazed's lab, wanted to follow up on strong hints from the scientific literature suggesting that the RNAi pathway is involved in the formation of heterochromatin. Other researchers had shown deletion of factors in the RNA interference pathway disrupts heterochromatin formation. And an MIT group found nearly a dozen small RNAs that exactly matched the DNA in the centromeres of fission yeast, which have three humanlike chromosomes.Verdel took a cue from the way RNAi works on messenger RNA. The small RNAs hook up with a protein complex called RISC and guide it to a complementary section of messenger RNA, where RISC initiates inactivation. Verdel tagged candidate proteins and screened them to see which ones had small RNA partners. The pilot screen identified Chp1, which Grewal's lab knew to be active early on in making heterochromatin. In addition, they identified two other required proteins in the complex, with the mass spectroscopy expertise of postdoc Scott Gerber and Steven Gygi, HMS assistant professor of cell biology, both co-authors on the paper. They named the complex RITS, for RNA-induced initiation of transcriptional gene silencing. It shares a protein with RISC and seems to work in a similar way, using small RNAs to guide it to a complementary spot on the genome. The RITS complex carries small RNAs whose four-letter sequences are exact complements of the DNA region they target. The complex cannot find that part of the genome without them. No one knows how the small RNAs in RITS attach to the genome--directly to the DNA or to newly formed RNAs that have not broken free. Also unknown are the additional steps that bridge the RITS complex to other heterochromatin proteins. The long-term gene silencing of heterochromatin helps give rise to a layer of inherited properties beyond the underlying genetic code, a phenomenon known as epigenetic inheritance, said Moazed. Dividing cells with identical genomes can retain their different identities as liver cells or blood cells in part by passing along swaths of silenced genes. Epigenetic errors have been implicated in some diseases, such as cancer and diabetes. And environmental factors may act upon epigenetic factors to cause disease. "For the last 30 years, the fundamental idea has been that genes are turned on and off by proteins that recognize specific DNA sequences," Moazed said. "It's still true for many genes that regulation is initiated by the action of site-specific DNA-binding proteins. This work tells you another way you can target genes and change expression states. It's powerful. It gives you enormous specificity with short DNA sequences." --Carol Cruzan Morton |
