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Abstract
For most of us, the phrase "Human Genome Project" conjures up images of vast amounts of nucleotide sequences, of impending insight into disease mechanisms, and, perhaps, even of individually tailored medicine. But one of the less touted opportunities presented by the genome project is the unprecedented potential to study chromosomes and genomes in their entirety - something simply not possible with the data from single-gene experiments so prevalent in the past 20 years.
| The Genome Project sheds light on the genetic ruler. |
One such genome-based study, presented in October 2000 at the American Society of Human Genetics annual meeting in Philadelphia, Pennsylvania, compares physical and genetic distances on human chromosomes.
Nearly a century ago, Thomas Hunt Morgan realized that recombination frequencies reflected the physical distance between two mutations. Since then, chromosomal map distances have been measured in centiMorgans (cM), where 1 cM is equal to 1% recombination. And though researchers have known for a while that it isn't strictly true, many assume that the recombination rate is uniform across a chromosome, thus viewing centiMorgans as a de facto ruler for physical distances.
| How proportional are centiMorgans and megabases? |
Now, for the first time, scientists can test the validity of this assumption over large portions of the genome by directly comparing real physical distances on a chromosome, measured in megabases (mb), to genetic distances, measured in centiMorgans. And while their findings might not be surprising, they are exciting for anyone interested in understanding the chromosome as a functional unit of biology.
Taking advantage of the nearly completed human genome sequence, James Weber from the Center for Medical Genetics in Marshfield, Wisconsin, and his collaborators compared the physical and genetic maps, using over 8,000 short tandem repeat polymorphisms (also called microsatellites), from eight large CEPH (Centre d'Etude du Polymorphisme Humain) families, representing 184 meioses.
| Weber's team found recombination deserts and jungles. |
Because the genome sequence is still a work in progress, Weber's team used only sequence contigs larger than 2 mb and whose gene order matched that of the genetic map. Within these limitations, the researchers were able to analyze about two-thirds of the euchromatic portion of the genome. They found that the recombination rates varied widely along even short distances on the chromosomes, as well as between male and female chromosomes. They found several regions of the genome, spanning more than 5 mb, that showed no recombination events - a rate of 0.0%. They refer to these regions as recombination deserts. In contrast, the highest intensity of recombination detected was in males at 13 cM per mb; these high-recombination regions are referred to as jungles. The highest intensity in females was 10.8 cM per mb.
In addition to the patterns of recombination differing between males and females, the overall rate is uneven as well. In females, the average rate is 1.0 cM per mb and in males it is 1.6 cM per mb. The reasons for this difference remain unclear.
| How hot are the hot spots? |
Weber emphasizes that their work is only a long range analysis with recombination rates averaged over several megabases. This means that the rate across any given jungle could be uniform or there could be recombination hot spots interspersed with relative deserts. Noting that there is good evidence from other studies that there are 1 or 2 kb recombination hot spots in humans, Weber says "The rates of recombination in those hot spots probably greatly exceed 13 cM per mb. So, at a very minimum, there are two orders of magnitude difference in recombination rates across the genome, and it could well be three or four or five orders of magnitude difference."
It is unclear, says Weber, what causes the differences between the deserts and jungles. The only consistent indicator of recombination frequencies they identify is an increase in the rate of recombination with increasing distance from the centromere in metacentric chromosomes. But even this indicator only holds true in males, since the rate in females varies up and down along the length of the chromosome arms.
| The cause of hot spots is a mystery. |
Looking for what might be causing the hot spots, Weber's team examined GC content, the frequency of Alu repeats, and the levels of marker heterozygosity. They are currently looking at the gene density. But they have not yet found any strong correlations.
In contrast to this, Jacek Majewski and Jurg Ott at the Laboratory of Statistical Genetics at Rockefeller University in New York, in a recent study, found a significant correlation on chromosome 22 between long tandem GT repeats and increased recombination frequencies.
| Chromosome 22 may have hot spots of long tandem GT repeats. |
However, in Weber's analysis this correlation only existed on chromosome 22, and the association there wasn't particularly strong. Ott, who wasn't present at the American Society for Human Genetics meeting, declined to comment on the discrepancy between the two studies.
Karl Broman, a professor of biostatistics in the Department of Biostatistics at the School of Public Health at Johns Hopkins University in Baltimore, Maryland, and one of Weber's collaborators, suggests that if the GT repeats were actually causing the increased recombination rate, then this association should be found throughout the genome. But, he concludes that they really don't know what is causing the variations in recombination intensity within a chromosome or between the sexes.
"We can't explain it," says Weber, "but we can use the information - that is the most important outcome of our study."
| The search narrows faster when disease genes lie in jungles. |
When researchers want to identify a disease gene, they use a technique called association mapping in which they winnow down the chromosomal region shared by individuals with the disease. As the shared region passes through generations, it tends to get broken up by recombination events into smaller and smaller pieces. By tracking the smallest region shared by individuals with the disease, scientists can identify the gene locus involved. But as Weber points out, if the disease gene occurs in a recombination desert, then the chromosomal region of interest will tend to remain intact over the generations, forcing researchers to look at a larger number of subjects in order to narrow down the actual locus. By contrast, if the disease gene occurs in a jungle, then the region of interest may narrow quickly and the researcher will likely need a higher density of chromosomal markers to track it.
This is where the new work is particularly helpful. With each region of the genome characterized in terms of local recombination rates, researchers who want to identify a disease gene can design their study accordingly, knowing at the outset if they are likely to need extra subjects or extra markers. To help researchers with this task, the Marshfield team will put the recombination frequency details for each chromosome on their Web site; the information for chromosome 21 is already available.
| Broman just needs to know the details. |
While this newly available data has the potential to change how genome researchers approach their work, in the end, perhaps Broman sums up the new work best: "My primary reason for studying this is the fact that recombination is important; we owe it to pay homage to the process of recombination and learn what is going on."
Rabiya S. Tuma is a freelance science writer based in Oregon and New York.
Frederick H. Carlson is a professional artist and illustrator whose clients include The Saturday Evening Post, Baltimore Sun and Pittsburgh Magazine.
Center for Medical Genetics - includes several human genetics resources for researchers.
Web Resources of Genetic Linkage Analysis - the Ott lab home page offers information on tools for genetic analyses.
Linkage Maps - an introduction to this genetic analysis, which begins with the work of Morgan.
Mapping in the Mouse: An Overview - this section of Mouse Genetics: Concepts and Applications by Lee Silver provides extensive background and experimental information on genetic mapping.
Links between Replication, Recombination and Genome Instability in Eukaryotes - examines the role that double-strand breaks play in these processes. From Trends in Biochemical Sciences, 2000, 25:4:196-200. Full text available from BioMedNet.
Recombination at Work for Meiosis - a review of the molecular mechanisms that lead to recombination. From Current Opinion in Genetics & Development, 1998, 8:200-211. Full text available from BioMedNet.
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