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A No-Nonsense Approach to Gene Relationships
by Siri Carpenter
Like a cassette in a tape deck, DNA is especially vulnerable to damage while it is being copied. A particular protein modification is known to protect cell integrity during replication, but despite efforts by several well-established laboratories, the trigger for this event has been a mystery.
Using a technique they developed to assemble large-scale gene-interaction databases, HHMI investigator Jonathan S. Weissman, HHMI postdoctoral fellow Sean Collins, and colleague Nevan Krogan—all at the University of California, San Francisco (UCSF)— discovered more quickly than other labs that the mystery protein is an enzyme called Rtt109 (see sidebar page 2, "The Protective Trigger").
Score one for E-MAP, a technique the scientists unveiled in 2005 to enhance studies of gene-gene, or epistatic, interactions. E-MAP stands for epistatic miniarray profiles. "It provides functional information that you just can't get any other way," notes Harvard Medical School biochemist Kevin Struhl. "It provides more detailed and comprehensive information than smaller studies can."
Weissman explains its purpose: "E-MAP is an automated technique to rapidly and systematically catalog how individual genes work together in a cell." Traditionally, biologists study gene interactions in yeast by eliminating or damaging an individual gene in a laboratory cell sample, pairing the resulting mutant with others, and observing whether the cells live or die. The drawback of this method is that it is slow and painstaking, and it requires subjective choices: which genes to select for study, which mutants to pair with which others.
For example, the budding yeast, Saccharomyces cerevisiae, contains about 6,000 genes. To analyze every gene-gene interaction would mean testing a daunting 18 million gene pairs. Scientists have devoted years to scrutinizing a few gene relationships of interest, knowing that, as a practical matter, they are ignoring others. Not necessary with E-MAP.
Krogan compares E-MAP to finding the light switch after stumbling around with just a flashlight. "With a flashlight, you see things in bits and pieces. With the lights on, you see how everything is connected."
To develop their most recent E-MAP, the UCSF group selected 743 genes in S. cerevisiae that code for a group of proteins involved in maintaining, replicating, and translating DNA to RNA. The team created double mutants from every possible combination of the genes—more than 200,000 gene pairs. Using software they developed, they compared the double mutants' growth rates with growth rates for single mutants. The result, detailed in an advance online publication in the journal Nature on February 21, 2007, was an atlas of how every gene they tested communicates with the others.
Illustration: Rachel Salomon