Regional physical maps

BACs represent the state-of-the-art technology for such large-insert DNA library development. It has been demonstrated that BAC libraries are invaluable and desirable genetic resources for all kinds of modern structural, functional, and evolutionary genomics research. Genome-wide, as well as regional, physical maps of the human genome from BACs have been developed in different laboratories. 

Fig. 4. Schematic organization of the Shaker K channel gene. The coordinates of the physical map are as in [9]. The direction of transcription is indicated by arrows. Approximate location of exons is given by boxes. Open box corresponds to noncoding exons, lettered boxes to alternative amino-terminal ends of Shaker channel proteins and the core region, respectively, numbered boxes to the two alternative carboxy-terminal ends. Exon numbers are as in [53].

DNA has been substituted in one strand.98 Since distances can be measured accurately on the electron micrographs, rather precise ( 50-100 bp) physical maps can be obtained. The chromosome map of phage K was mapped in this way initially now its complete nucleotide sequence is known. Another electron microscopic method is useful for location of AT-rich regions that denature readily. In a suitable concentration of formamide these regions melt to form visible single-stranded denaturation loops similar to the bubbles in Figure 26-6. 

Figure 28-11 Genetic and physical map of the X phage genome. After Szybalski. See Honigman et al.255 for a more detailed diagram of the immunity region. The gene for the lambda repressor is labeled C[.

Recently, a continuous physical map of the entire mouse k locus has been produced (George et al., 1995 Zocher et al., 1995 Kirschbaum et al., 1996 Schupp et al., 1997). The size of the locus is between 3 and 3.5 Mb. There is evidence for about 140 VK gene segments in the locus and a number of others are outside the locus. Individual members of a mouse VK family are frequently clustered in the same region (Heinrich et al., 1984 D Hoostelaere et al., 1988), but interspersion with members of different families is not uncommon (Zocher et al., 1995). Some... 

Hofker, M.H., Walter, M.A., Cox, D.W. (1989). Complete physical map of the human heavy chain constant region gene complex. Proc. Natl. Acad. Sci. USA 86,5567-5571. 

Matsuda, F., Shin, E.K., Nagaoka, H., Matsumura, R., Haino, M., Fukita, Y., Taka-ishi, S., Imai, T., Riley, J.H., Anand, R., Soeda, E., Honjo, T. (1993). Structure and physical map of 64 variable segments in the 3 0.8-megabase region of the human immunoglobulin heavy-chain locus. Nature Genet. 3, 88-94. 

Poltorak A, Smirnova I, He X, Liu MY, Van Huffel C, McNally O, Birdwell D, Alejos E, Silva M, Du X, Thompson P, Chan EK, Ledesma J, Roe B, Clifton S, Vogel SN, Beutler B. Genetic and physical mapping of the Lps locus identification of the toll-4 receptor as a candidate gene in the critical region. Blood Cells Mol Dis 1998 24(3) 340-355. 

Heyraud, F., Serror, P, Kuntz, M., Steinmetz, A., and Heizmann, P, Physical map and gene localization on sunflower (Helianthus annuus) chloroplast DNA evidence for an inversion of a 23.5-kbp segment in the large single copy region, Plant Mol. Biol., 9, 485 -96, 1987. 

B. Locating Gene Functions - The goal of mapping a mutant is to determine what function is affected by the mutation, and where that function is located on the physical map. Consequently, the protein or protein region responsible for the function can be determined. The quest to Identify the gene function(s) required for viral transformation and how that function is controlled has been of special interest. 

Temperature-sensitive Mutants - A number of temperature-sensitive mutants of SV40 have been analyzed. Those found defective in the complementation A group and the physical map regions which code for the early proteins (T antigen and t) were also found defective in their ability to transform cells. The temperature-sensitive transformation defect was reversible at permissive temperatures, i.e., transformed colonies appeared. Mutants defective in the formation of late proteins (viral structural proteins) were able to transform cells. Therefore, functional early proteins are required to effect and maintain transformation. The early proteins necessary for transformation also permit viral DNA replication and the stimulation of host cell DNA synthesis. The exact biochemical functions required for transformation have not yet been determined. 

The story of CF (box 5-D) is one of the most straightforward that can be expected, but it nonetheless required enormous effort. From 1985 to 1989, laboratories throughout the world labored to find the gene. One reason for the protracted search was that the physical maps and regional sequencing had to be done de novo. Once complete maps of the human genome are constructed, similar searches should be much faster and less costly. 

Schematic drawing showing the human Y chromosome physical map. In all, 196 individual YAC clones were assembled into 10 contiguous segements separated by nine short gaps. The location of several known genes and the putative centromere region are shown.

The human ecNOS gene was assigned to the 7q35-q36 region of chromosome 7 (Marsden et al., 1993 Xu et al., 1994b Robinson etal., 1994). Comparison with genetic or physical maps of human chromosomes fails to define common or rare human disease conditions that are known to map... 

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