Partial Sequencing To Facilitate Mapping, Gene Identification
Correlating mapping data from different laboratories has been a problem because of differences in generating, isolating, and mapping DNA fragments. A common reference system designed to meet these challenges uses partially sequenced unique regions (200 to 500 bp) to identify clones, contigs, and long stretches of sequence. Called sequence tagged sites (STSs), these short sequences have become standard markers for physical mapping.
Because coding sequences of genes represent most of the potentially useful information content of the genome (but are only a fraction of the total DNA), some investigators have begun partial sequencing of cDNAs instead of random genomic DNA. (cDNAs are derived from mRNA sequences, which are the transcription products of expressed genes.) In addition to providing unique markers, these partial sequences [termed expressed sequence tags (ESTs)] also identify expressed genes. This strategy can thus provide a means of rapidly identifying most human genes. Other applications of the EST approach include determining locations of genes along chromosomes and identifying coding regions in genomic sequences.
End Games: Completing Maps and Sequences; Finding Specific Genes
Starting maps and sequences is relatively simple; finishing them will require new strategies or a combination of existing methods. After a sequence is determined using the methods described above, the task remains to fill in the many large gaps left by current mapping methods. One approach is single-
chromosome microdissection, in which a piece is physically cut from a chromosomal region of particular interest, broken up into smaller pieces, and amplified by PCR or cloning (see DNA Amplification above). These fragments can then be mapped and sequenced by the methods previously described.
Chromosome walking, one strategy for filling in gaps, involves hybridizing a primer of known sequence to a clone from an unordered genomic library and synthesizing a short complementary strand (called walking along a chromosome). The complementary strand is then sequenced and its end used as the next primer for further walking; in this way the adjacent, previously unknown, region is identified and sequenced. The chromosome is thus systematically sequenced from one end to the other. Because primers must be synthesized chemically, a disadvantage of this technique is the large number of different primers needed to walk a long distance. Chromosome walking is also used to locate specific genes by sequencing the chromosomal segments between markers that flank the gene of interest (Fig. 13: Cloning a Disease Gene by Chromosome Walking).
The current human genetic map has about 1000 markers, or 1 marker spaced every 3 million bp; an estimated 100 genes lie between each pair of markers. Higher-
resolution genetic maps have been made in regions of particular interest. New genes can be located by combining genetic and physical map information for a region. The genetic map basically describes gene order. Rough information about gene location is sometimes available also, but these data must be used with caution because recombination is not equally likely at all places on the chromosome. Thus the genetic map, compared to the physical map, stretches in some places and compresses in others, as though it were drawn on a rubber band.
The degree of difficulty in finding a disease gene of interest depends largely on what information is already known about the gene and, especially, on what kind of DNA alterations cause the disease. Spotting the disease gene is very difficult when disease results from a single altered DNA base; sickle cell anemia is an example of such a case, as are probably most major human inherited diseases. When disease results from a large DNA rearrangement, this anomaly can usually be detected as alterations in the physical map of the region or even by direct microscopic examination of the chromosome. The location of these alterations pinpoints the site of the gene.
Identifying the gene responsible for a specific disease without a map is analogous to finding a needle in a haystack. Actually, finding the gene is even more difficult, because even close up, the gene still looks like just another piece of hay. However, maps give clues on where to look; the finer the maps resolution, the fewer pieces of hay to be tested.
Once the neighborhood of a gene of interest has been identified, several strategies can be used to find the gene itself. An ordered library of the gene neighborhood can be constructed if one is not already available. This library provides DNA fragments that can be screened for additional polymorphisms, improving the genetic map of the region and further restricting the possible gene location. In addition, DNA fragments from the region can be used as probes to search for DNA sequences that are expressed (transcribed to RNA) or conserved among individuals. Most genes will have such sequences. Then individual gene candidates must be examined. For example, a gene responsible for liver disease is likely to be expressed in the liver and less likely in other tissues or organs. This type of evidence can further limit the search. Finally, a suspected gene may need to be sequenced in both healthy and affected individuals. A consistent pattern of DNA variation when these two samples are compared will show that the gene of interest has very likely been found. The ultimate proof is to correct the suspected DNA alteration in a cell and show that the cells behavior reverts to normal.
Model Organism Research
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Mapping and