Call it a molecular security belt. A newfound protein restraint protects a valuable stretch of highly repetitive DNA, independent of the silencing power of the well-known Sir2 chromatin-modifying enzyme. The protein tether confines the easily corrupted length of chromosome next to the inner nuclear membrane, where it is cloistered from the rest of the genome.
“For years, people have used silencing of genes within repeats as an assay for genomic stability of the repeats, but silencing is only a surrogate,” said Danesh Moazed, a Howard Hughes investigator, HMS professor of cell biology, and senior author of this study in the Dec. 4 Nature. Chromatin silencing alone was not sufficient to safeguard genomic integrity, at least in yeast. Securing the DNA at the membrane also was necessary to prevent destructive recombination. “The two things have to work together,” he said.
The findings come from studies of a part of chromosome 12 stacked end-to-end with hundreds of repeat genes that spit out the crucial RNA parts of ribosomes, the protein-making machinery of the cell. These are the busiest genes in fast-growing yeast, accounting for up to 80 percent of transcription. The repetitive DNA is especially prone to recombination, which could disable the life-sustaining gene activity.
First author Karim Mekhail began the project by following up on a tantalizing piece of data from a previous study in the lab. A pair of membrane proteins had showed up in the extensive network of protein–protein interactions catalogued for gene silencing. The research was part of a continuing collaboration with co-author Steven Gygi, HMS associate professor of cell biology, who has developed highly sensitive mass spectrometry protein identification techniques. The data hinted that the DNA repeats are hooked to the inner nuclear membrane.
“The big question is why DNA is nonrandomly located in the nucleus,” said Mekhail, a postdoctoral fellow in the Moazed lab. “The nucleus holds a huge amount of highly compacted linear genomic information. But what scientists have realized over the last couple of decades is that there is a lot of order to the position of the DNA in relation to the membrane.”
The critical experimental juncture came when Mekhail and Moazed separated chromatin silencing from recombination suppression in their minds while trying to make sense of their results and then showed that tethering alone could inhibit recombination.
Unrestrained, the easily corrupted portion of the chromosome drifted around the nucleus, its susceptible genetic parts at risk of being switched or stripped (see illustration). The protein tether, dubbed CLIP, also may align and stabilize the vulnerable repeats when the DNA replicates for cell division.
“What’s really new is how the spatial organization of the nuclear envelop protects against genomic instability,” said Susan Gasser, director of the Friedrich Miescher Institute for Biomedical Research in Basel, Switzerland.
In a related Oct. 24 Science paper, Gasser’s group reported that some DNA strand breaks are shunted to nuclear pores for repair. “The same way that protein function depends on its three-dimensional structure, genome function depends upon its folding within the nucleus,” she said. The specialized periphery roles in yeast probably translate to internal nuclear subcompartments in mammals, she said.
Students may contact Danesh Moazed at danesh@hms.harvard.edu for more information on this and other lab projects.
Conflict Disclosure: The authors declare no conflicts of interest.
Funding Sources: The National Institutes of Health and the Canadian Institutes of Health Research.
