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Structures of naturally evolved CUP1 tandem arrays in yeast indicate that these arrays are generated by unequal nonhomologous recombination.

Zhao Y, Strope PK, Kozmin SG, McCusker JH, Dietrich FS, Kokoska RJ, Petes TD - G3 (Bethesda) (2014)

Bottom Line: In the yeast Saccharomyces cerevisiae, most strains contain tandemly duplicated copies of CUP1, a gene that encodes a copper-binding metallothionein.By screening 101 natural isolates of S. cerevisiae, we identified five different types of CUP1-containing repeats, as well as strains that only had one copy of CUP1.A comparison of the DNA sequences of these strains indicates that the CUP1 tandem arrays were generated by unequal nonhomologous recombination events from strains that had one CUP1 gene.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina 27710.

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Southern analysis of the CUP1 genes in 13 yeast strains. Genomic DNA from each strain was treated with EcoRI. There are no recognition sites for EcoRI within the CUP1 repeats (Figure 2A). The fragments were separated by gel electrophoresis, transferred to a membrane, and hybridized to a probe containing the CUP1 sequences. The lanes labeled S1 and S2 on the left side of the figure are ethidium bromide-stained fragments representing size standards (Hyperladders VI and I from Bioline). S2 in the gel on the right side of the figure is the same ladder hybridized to a ladder-specific probe. The samples in lanes 1−13 are: 1 (YJM189), 2 (YJM271), 3 (YJM456), 4 (YJM693), 5 (YJM969), 6 (YJM972), 7 (YJM978), 8 (YJM996), 9 (YJM1549), 10 (YJM1307), 11 (S288c), 12 (W303-1A), and 13 (YJM789). The fragment sizes in lanes 1−13 are in Table 1.
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fig5: Southern analysis of the CUP1 genes in 13 yeast strains. Genomic DNA from each strain was treated with EcoRI. There are no recognition sites for EcoRI within the CUP1 repeats (Figure 2A). The fragments were separated by gel electrophoresis, transferred to a membrane, and hybridized to a probe containing the CUP1 sequences. The lanes labeled S1 and S2 on the left side of the figure are ethidium bromide-stained fragments representing size standards (Hyperladders VI and I from Bioline). S2 in the gel on the right side of the figure is the same ladder hybridized to a ladder-specific probe. The samples in lanes 1−13 are: 1 (YJM189), 2 (YJM271), 3 (YJM456), 4 (YJM693), 5 (YJM969), 6 (YJM972), 7 (YJM978), 8 (YJM996), 9 (YJM1549), 10 (YJM1307), 11 (S288c), 12 (W303-1A), and 13 (YJM789). The fragment sizes in lanes 1−13 are in Table 1.

Mentions: Variation in the number of CUP1 repeats in tandem arrays of different yeast strains has been observed previously by Southern analysis (Welch et al. 1983). In addition, in the analysis of the 100-genome strains, estimates of the numbers of repeats per strain were made based on the number of times CUP1 sequences were present relative to single-copy sequences (P. K. Strope, D. A. Skelly, S. G. Kozmin, G. Mahadevan, E. A. Stone, P. M. Magwene, F. S. Dietrich, and J. H. McCusker, personal communication). We used Southern analysis to determine the number of repeats in 10 strains that were part of the 100-genome strain analysis, as well as three other yeast strains (S288c, W303-1A, and YJM789). For this analysis, genomic DNA was treated with EcoRI which does not have a recognition sequence within the repeats (Figure 2A). Southern analysis of the strains is depicted in Figure 5.


Structures of naturally evolved CUP1 tandem arrays in yeast indicate that these arrays are generated by unequal nonhomologous recombination.

Zhao Y, Strope PK, Kozmin SG, McCusker JH, Dietrich FS, Kokoska RJ, Petes TD - G3 (Bethesda) (2014)

Southern analysis of the CUP1 genes in 13 yeast strains. Genomic DNA from each strain was treated with EcoRI. There are no recognition sites for EcoRI within the CUP1 repeats (Figure 2A). The fragments were separated by gel electrophoresis, transferred to a membrane, and hybridized to a probe containing the CUP1 sequences. The lanes labeled S1 and S2 on the left side of the figure are ethidium bromide-stained fragments representing size standards (Hyperladders VI and I from Bioline). S2 in the gel on the right side of the figure is the same ladder hybridized to a ladder-specific probe. The samples in lanes 1−13 are: 1 (YJM189), 2 (YJM271), 3 (YJM456), 4 (YJM693), 5 (YJM969), 6 (YJM972), 7 (YJM978), 8 (YJM996), 9 (YJM1549), 10 (YJM1307), 11 (S288c), 12 (W303-1A), and 13 (YJM789). The fragment sizes in lanes 1−13 are in Table 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4232551&req=5

fig5: Southern analysis of the CUP1 genes in 13 yeast strains. Genomic DNA from each strain was treated with EcoRI. There are no recognition sites for EcoRI within the CUP1 repeats (Figure 2A). The fragments were separated by gel electrophoresis, transferred to a membrane, and hybridized to a probe containing the CUP1 sequences. The lanes labeled S1 and S2 on the left side of the figure are ethidium bromide-stained fragments representing size standards (Hyperladders VI and I from Bioline). S2 in the gel on the right side of the figure is the same ladder hybridized to a ladder-specific probe. The samples in lanes 1−13 are: 1 (YJM189), 2 (YJM271), 3 (YJM456), 4 (YJM693), 5 (YJM969), 6 (YJM972), 7 (YJM978), 8 (YJM996), 9 (YJM1549), 10 (YJM1307), 11 (S288c), 12 (W303-1A), and 13 (YJM789). The fragment sizes in lanes 1−13 are in Table 1.
Mentions: Variation in the number of CUP1 repeats in tandem arrays of different yeast strains has been observed previously by Southern analysis (Welch et al. 1983). In addition, in the analysis of the 100-genome strains, estimates of the numbers of repeats per strain were made based on the number of times CUP1 sequences were present relative to single-copy sequences (P. K. Strope, D. A. Skelly, S. G. Kozmin, G. Mahadevan, E. A. Stone, P. M. Magwene, F. S. Dietrich, and J. H. McCusker, personal communication). We used Southern analysis to determine the number of repeats in 10 strains that were part of the 100-genome strain analysis, as well as three other yeast strains (S288c, W303-1A, and YJM789). For this analysis, genomic DNA was treated with EcoRI which does not have a recognition sequence within the repeats (Figure 2A). Southern analysis of the strains is depicted in Figure 5.

Bottom Line: In the yeast Saccharomyces cerevisiae, most strains contain tandemly duplicated copies of CUP1, a gene that encodes a copper-binding metallothionein.By screening 101 natural isolates of S. cerevisiae, we identified five different types of CUP1-containing repeats, as well as strains that only had one copy of CUP1.A comparison of the DNA sequences of these strains indicates that the CUP1 tandem arrays were generated by unequal nonhomologous recombination events from strains that had one CUP1 gene.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology and University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina 27710.

Show MeSH
Related in: MedlinePlus