- Posted Wednesday August 13, 2003
Novel genomics study compares 13 vertebrate species and gains insight into function and evolution of the human genome
Aug. 21, 2003
In one of the most thorough and systematic comparisons of vertebrate genomic sequences performed to date, a team led by the National Human Genome Research Institute (NHGRI) reported results that demonstrate how such comparisons can reveal functionally important parts of the human genome beyond the genes themselves.The team, which includes Dr. Jeffrey Touchman -- an Investigator and director of the sequencing facility at the Translational Genomics Research Institute, Phoenix -- published its findings in the Aug. 14 issue of Nature.
The authors generated more than 12 million base pairs of DNA sequence from twelve selected vertebrate species including human, chimpanzee, baboon, cat, dog, cow, pig, rat, mouse, chicken, zebrafish, and two species of pufferfish (Fugu, Tetraodon). They targeted a 1.8 million base pair region of human chromosome 7, which contains ten genes including the cystic fibrosis gene, and sequenced this region in each species. This represents the most diverse collection of large blocks of similar vertebrate DNA sequence generated to date.
"One of the things we examined was how much of our genome sequence was 'conserved' across organisms," Touchman said.
As organisms evolved into species, specific sequences were conserved, or selected for retention in the genome, over millions of years of evolution. One important discovery emanating from this multi-species sequence analyses was the presence of substantial numbers of previously unidentified DNA segments that are conserved across a wide range of species, but which, unlike genes, do not code for proteins. Most of these conserved, non-coding regions could be uncovered only by using the sequences from multiple species. While the precise function of these elements is not yet known, the fact that they have been preserved over millions of years of evolution suggests they may be indispensable to the organism.
"Comparison is a fundamental tool in biology," Touchman said. "By comparing DNA sequence from several different species, we gain tremendous power to identify many of the biologically functional parts of our genome that might otherwise remain anonymous." Touchman said.
This multi-species sequence generation and analysis has allowed researchers to gain insight into vertebrate evolution, confirm phylogenies, and reveal conserved elements in non-coding regions. It also illustrates differences in the relative contributions of the various changes that have uniquely sculpted each species' genome. These findings point to the complex ways that evolution has used millions of years of genetic alterations to render each species' genome into its modern-day form.
Dr. Touchman and his collaborators plan to continue comparative analyses of genomes to gain insight into genetic factors that contribute to human disease.
The mission of the Translational Genomics Research Institute (TGen) is to make and translate genomic discoveries into advances in human health. "Translational research" is a relatively new field employing innovative advances arising from the Human Genome Project to apply to the development of diagnostics, prognostics and therapies for cancer, neurologic disorders, diabetes and other complex diseases.
The UCSC team who contributed to this research study has constructed a specialized component of its Web site, genome.ucsc.edu, for viewing the sequences generated from the multiple species, as well as for examining the results of the comparative analyses reported in the study.
The use of multi-species sequences for identifying functionally important regions of the human genome, as described in the Nature paper, will be a prominent component of an NHGRI-sponsored program called the ENCylopedia Of DNA Elements (ENCODE) project (www.genome.gov/Encode). The ultimate goal of the ENCODE project is to catalog all functional elements in the human genome sequence, thereby deepening our understanding of human biology and stimulating the development of new strategies for preventing and treating disease.
For more information on Dr. Touchman and the comparative genomic research projects at TGen go to: www.tgen.org