Expanding the Ranks of Vertebrate Genomes

Filling in evolutionary blanks is just the first feat for the rat and chicken genomes.

By | September 1, 2006

When the brown Norway rat1 and the red jungle fowl2 joined the ranks of the sequenced in 2004, two unsung heroes of experimental biology finally got their due. Although the projects met with some resistance at the start, a genetics toolbox has been assembled that is worthy of these animals' research status, and scientists are starting to succeed in applying its contents.

Used in countless drug and toxicity studies, the rat has long been a pharmacological workhorse, says Richard Gibbs at the Baylor College of Medicine in Houston. But unlike in mice, rat genes could not be knocked out to reveal their associated traits, so the rat lagged behind as a genetic model. "Quite simply, [the genome sequence] revolutionized the work you could do in rats," says Howard Jacob at the Medical College of Wisconsin and director of the Rat Genome Database.

The chicken and its easily scrutinized eggs have been invaluable in enabling researchers to study embryonic development and human diseases such as muscular dystrophy, yet the bird?s genome was largely uncharted territory. When the genome was sequenced by the International Chicken Sequencing Consortium, led by Washington University in St. Louis, the common bird "became a very exciting tool from a comparative evolution approach," says Paul Siegel at Virginia Polytechnic Institute.

Making Comparisons

With their strategic positions on the evolutionary tree, both rat and chicken sequences have proven their worth in comparative studies. Scientists used the rat to triangulate the relationship between mouse and human genomes, thus isolating the nearly 40% of nucleotides conserved between the three as the essence of a mammal, says lead investigator George Weinstock at Baylor.

Humans and birds are thought to have diverged 310 million years ago, compared to the roughly 75 million years between rats and humans, and the chicken has provided the best out-group to date for studying human evolution. "The evolutionary distance between chicken and mammal suppresses the random similarity of the genomes down to almost nothing," says Jerry Dodgson at Michigan State University, who was part of the consortium.

Dodgson says that of the 5% of sequence conserved between humans and chickens, he was surprised to find that only 2% corresponded to protein-coding genes. "We kind of thought that?s where the action is. Yet what the comparisons [are] telling us [is] that?s where only half the action is," Dodgson says. As a result, researchers have found DNA regulatory elements and increasingly, noncoding microRNAs conserved in chickens and humans that may play roles in regulation or even chromosomal structure, Dodgson says. By comparing the structures and conservation patterns of both genomes, others are beginning to understand how gene deserts function in humans.3

Even as they are being used to improve human genome maps, the rat and chicken genomes are aiding species-specific research and revealing the power of the sequencing techniques used to create them. Phenotype analysis had already provided a bit of a genetic map for the rat and chicken. Researchers had been honing in on genetic loci associated with complex and quantitative traits such as cell metabolism, hypertension, and kidney function in rats, for example, but with the genome sequenced, those who wish to do positional cloning now have a reference to pinpoint genetic causes of disease, says Tim Aitman at Imperial College London. For agriculturists, the chicken?s genomic template has made it easier to connect desired traits to their genetic sources.

In sequencing both genomes, researchers combined the speed and cost-effectiveness of the whole-genome shotgun approach with the time-consuming comprehensiveness of the clone-by-clone approach. As a result, the rat consortium found a duplication rate of about 5% in rat genes, a feature that the whole-genome shotgun method failed to pick up in the mouse genome.

Stocking the Toolboxes

This combined approach allowed Aitman to recently implicate low copy numbers of the antibody receptor gene Fcgr-3 in glomerulo-nephritis, a complex immune-related disease, for both rats and humans.4 Once his team had narrowed its search to chromosome 13, and referenced the rat genome to pick the right gene, clone lengths from the sequencing project helped Aitman?s team count copies of the gene.

Researchers in the Czech Republic similarly used the genome sequence to locate an elusive chicken retrovirus receptor.5 Siegel and colleagues have identified loci connected to chicken growth and are now using the sequence to look for the specific genes.6

Besides its comparative value, says Glenn Tesler at the University of California, San Diego and a participant in the chicken genome project "people are interested in chicken in its own right ? we eat chickens, we raise chickens [for] eggs." Researchers initially believed that the chicken sequence would provide insight into the mechanisms of bird flu, though little evidence of this has been found so far. Dodgson says researchers are striving to improve sequence corresponding to the B loci (the bird equivalent of MHC in humans), which influence viral resistance.

The genetic toolbox for rats and chickens has been catching up with that of mice since the sequenced genome was published,7 says Edwin Cuppen at Hubrecht Laboratory in Utrecht, the Netherlands. Though the method is imprecise, researchers can now create a version of knockout rats by using ENU mutagenesis to produce random point mutations in male rats and then searching pools of offspring for a mutation to the gene of interest. As for chickens, researchers are increasingly using RNAi to genetically manipulate chick embryos in developmental studies. As more tools are developed, the uses for these model organisms should expand.

"When you do one of these genome sequences, you put so much out there for people that it goes in many, many different directions," says Weinstock. "You can?t possibly imagine all the things that can come out of it."

iganguli@the-scientist.com

Data derived from the Science Watch/Hot Papers database and the Web of Science (Thomson ISI) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age. Rat Genome Sequencing Project Consortium, "Genome sequence of the brown Norway rat yields insights into mammalian evolution," Nature, 428:493-521, 2004. (Cited in 300 papers) L.W. Hillier et al., "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution," Nature, 432:695-716, 2004. (Cited in 136 papers)

References

1. Rat Genome Sequencing Project Consortium, "Genome sequence of the brown Norway rat yields insights into mammalian evolution," Nature, 428:493-521, 2004. (Cited in 300 papers) 2. L.W. Hillier et al., "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution," Nature, 432:695-716, 2004. (Cited in 136 papers) 3. I. Ovcharenko, "Evolution and functional classification of vertebrate gene deserts," Genome Res, 15:137-45, 2005. 4. T.J. Aitman, et al., "Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans," Nature, 439:851-5, Feb. 16, 2006. 5. D. Elleder et al., "The receptor for the subgroup c avian sarcoma and leukosis viruses, Tvc, is related to mammalian butyrophilins, members of the immunoglobulin superfamily," J Virol, 79:10408-19, 2005. 6. G. Bourque et al., "Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages," Genome Res, 15:98-110, 2005. 7. B.M. Smits et al., "Rat genetics: the next episode," Trends Genet, 22:232-40, April 2006.

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