A Star is Born

Data derived from the Science Watch/Hot Papers database and the Web of Science (ISI, Philadelphia) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age. M. Adams et al., "The genome sequence of Drosophila melanogaster," Science, 287:2185-95, March 24, 2000. (Cited in 711 papers) G.M. Rubin et al., "Comparative genomics of the eurkaryotes," Science, 287:2204-15. (Cited in 333 papers) In 1999, Celera Genomics Group wanted to complete the human genome sequence. The company developed a novel method it called whole genome shotgun (WGS) sequencing; researchers believed it would revolutionize the process of sequencing. Moreover, the company had also just opened up a new facility, with 300 brand-new, out-of-the-box automated DNA sequencers, plus a crew of 50 to staff them. Yet instead of hitting the ground running, Celera decided to sequence a simpler genome, thereby simultaneously achieving proof of concept for WGS sequencing while working out the kinks of its new facility. The oft-studied Drosophila melanogaster fit the bill. "Drosophila is about 5% of the size of the human genome," says Mark Adams, Celera's vice president of bioinformatics and a key author on both Hot Papers.1,2 "From that perspective, when we looked at the number of days [delay] to complete the human genome by virtue of having done Drosophila first, it was something like 20 days--that's a modest delay to get a proof of principle, but to also get the Drosophila genome done would be quite useful." Photo: Courtesy of Celera Genomics WHAT THE BUZZ IS ALL ABOUT: Working out the Drosophila sequencing puzzle in the Celera lab. THE ARGUMENT FOR DROSOPHILA Drosophila's "great historical importance and the large research community that could benefit from the sequence were also important factors for choosing fly rather than another organism," continues Adams. He was right: the paper garnered more than 700 citations since publication. A second paper--a comparison of the genomes of Drosophila, Caenorhabditis elegans, and Saccharomyces cerevisiae--received more than 300 citations.2 The citations are probably due to Drosophila's usefulness as a model system, says staff scientist Susan Celniker, Lawrence Berkeley National Laboratory in California and codirector of the Berkeley Drosophila Genome Project. With a life span measured in weeks rather than years, the fruit fly is easy to experiment with; moreover, researchers can track a gene's effects throughout the animal's life span, she says. Another explanation: The surprising similarities between humans and flies make Drosophila even more important. At least 80 genes implicated in cancer have homologs in flies, Celniker says, and additional models exist for anemias and even Alzheimer disease. But perhaps the most important rationale is that Drosophila is a stepping-stone to other model organisms. "If you can nail down the function of your new gene in a fly, it can give you much better targeting of experiments to do in a mouse. You can do so many more experiments in a fly," says Celniker, who also helped author both papers. COMPARE AND CONTRAST The second Hot Paper is a comparative genomic analysis of Drosophila (fly), C. elegans (worm), and S. cerevisiae (yeast). The researchers also searched for orthologs of human disease genes in the fly. They picked those organisms because the full genomes were available, and because they gave a reasonably broad and representative overview of eukaryotes, says Adams. One question that drove the project, he says, was: "Where does complexity come from?" The fly and worm genomes are of similar size and about twice the size of yeast, but "flies can do more creative things [than worms]: they have more behaviors, more complicated development, they fly, they can see, and yet they have fewer genes than worms. So the next question is: 'How is variation of those activities encoded in genes?' And that presages the human [genome] analysis." Regarding complexity, the comparative analysis posed more questions than it answered, but the link with human disease genes turned up some interesting results. Adams' team was surprised to find that 177 of the 289 human disease genes studied had a Drosophila counterpart. "I think we were reasonably impressed with the level of conservation that there was between Drosophila and humans." A recent paper3 by Adams' group compared chromosome 16 in mice with corresponding regions in the human genome and found them to be remarkably alike. "The similarities are incredibly striking, with long blocks of shared homology. In many senses they are so close together that they're not different enough to be able to draw a contrast. Flies and humans are different enough that where things are conserved it's not simply a chance of evolution," says Adams. The comparative analysis identified various protein and enzyme families, which can be used to explore the molecular basis of fly biology. "It's a great way of setting up hypotheses, which I imagine have been tested over the past few years, as people pounce on these new genes and are trying to see how they fit into their favorite pathways," says Adams. "The genome sequence is a great way to ask a lot of questions, and it's a great way to answer a few questions," he continues. "That's one of the reasons it's been cited so much, perhaps." STAR ATTRACTION Drosophila's appeal as a model system has attracted thousands of researchers. Gerald Rubin, a Berkeley Laboratory codirector, estimates that number at 5,000, with probably 500 labs and an average of 10 people per lab. "Anybody studying a gene in Drosophila cites the genome paper," says Celniker. "Before, you had to map your gene using either genetics or P elements [a class of transposons found in Drosophila], and to figure out where it was, you'd have to clone it and determine the sequence. With the sequencing complete now, the task is to map your gene and determine its function." That achievement made numerous experiments possible. In the 1950s, Jerry Hirsch of the University of Illinois performed landmark experiments on Drosophila,4 demonstrating that specific chromosomal areas are tied to the tendency of an animal to go upward (negative geotaxis) or downward (positive geotaxis) in a vertical maze. But Hirsch could not identify the genes involved, because he was limited by the genetics technologies of the day, and because multiple genes influence behavioral differences. JUMP TO 2002 Ralph J. Greenspan, a fellow in experimental neurobiology at the Neurosciences Institute in San Diego, Calif., published work that showed how DNA microarrays can track differences in expression levels of genes in positive- and negative-geotaxic flies.5 Rather than trying to follow all available genes, the researchers focused on genes believed to be involved in nervous system function. They identified three genes associated with behavioral changes. Further experiments demonstrated that these genes had measurable effects on behavior when their expression levels were altered, as in Hirsch's lines. The results pinpoint genes underlying a complex polygenic behavior, something that eluded researchers using classical methods. "Without the microarrays we couldn't have done this at all. It would have been just fishing in the dark," says Greenspan. It's just that sort of futility that the P- element Screen/Gene Disruption Project--another result of the Drosophila genome sequencing--hopes to prevent. Run by Hugo Bellen, a Howard Hughes Medical Institute investigator at the Baylor College of Medicine, the project uses P elements to create single-gene-knockout fly lines. P elements, which contain terminal inverted repeats, create target site duplications when transposed and can cause genetic aberrations. To identify a new gene, researchers sequence the DNA surrounding the P element, and if novel, the gene is added to the list for the knockout line. Bellen's team has completed 4,071 genes so far; they plan to reach about 10,000 of the approximately 13,000 Drosophila genes believed to exist. The last 3,000 or so are genes that contain a large number of repeats, making them more effort-intensive. Beyond 10,000, "it's going to have diminishing returns," says Bellen. Baylor's Web site makes the P-Screen Database available to researchers (http:// flypush.imgen.bcm.tmc.edu/pscreen/). Without such a resource, researchers are reduced to mapping the gene using in situ hybridization. At one point, it took 18 months from identifying a Drosophila homolog of a human gene to mapping the gene in the fly. "Now it's reduced to not even a day," Bellen says. The increased efficiency emerging from the genome project has added further impetus to the burgeoning field of Drosophila genetics. The sequencing project began as a warm-up for the human genome project, but the rush of Drosophila research activity figures to be only a taste of what is to come. The Berkeley lab is putting the finishing touches on the Drosophila genome, filling in gaps in the sequence's earlier version. The project focused on the euchromatin first because it contains a majority of the genes. The Berkeley team expects to publish the completed euchromatic portion of the genome, along with several companion papers describing the methodology used, by year's end. Jim Kling (jkling@nasw.org) is a freelance writer in Washington, DC. References 1. M. Adams et al., "The genome sequence of Drosophila melanogaster," Science 287:2185-95, March 24, 2000. (Cited in 711 papers) 2. G.M. Rubin et al., "Comparative genomics of the eu-karyotes," Science, 287:2204-15. (Cited in 333 papers) 3. R.J. Mural et al., "A comparison of whole genome shotgun-derived mouse chromosome 16 and the human genome," Science, 296:1661-71, 2002. 4. J. Hirsch et al., "Studies in experimental behavior genetics: IV. Chromosome analyses for geotaxis," Journal of Comparative Physiology, 55:732-9, 1962. 5. P. Daniel et al., "Identification of genes involved in Drosophila melanogaster geotaxis, a complex behavioral trait," Nature Genetics, 31:349-53, 2002.

A Star is Born

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