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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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Generation of a de novo duplication of CUP1 by unequal nonhomologous end-joining. A mechanism for the generation of a two-copy tandem array of CUP1 from a single CUP1 gene (similar to the duplication observed in S288c) is shown. We suggest that, during DNA replication, one fork is broken in the intergenic region between CIC1 and RUF5/CUP1/ARS810. The second fork is broken within RSC30. The nonhomologous end-joining of one broken end to the other (indicated by the dashed line) would produce the duplication. If the other broken ends are also joined, a deletion of RUF5/CUP1/ARS810 would be produced in the sister chromatid.
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fig8: Generation of a de novo duplication of CUP1 by unequal nonhomologous end-joining. A mechanism for the generation of a two-copy tandem array of CUP1 from a single CUP1 gene (similar to the duplication observed in S288c) is shown. We suggest that, during DNA replication, one fork is broken in the intergenic region between CIC1 and RUF5/CUP1/ARS810. The second fork is broken within RSC30. The nonhomologous end-joining of one broken end to the other (indicated by the dashed line) would produce the duplication. If the other broken ends are also joined, a deletion of RUF5/CUP1/ARS810 would be produced in the sister chromatid.

Mentions: All five classes of repeats can be explained by the duplication mechanism shown in Figure 8. We suggest that, during replication of a chromosome with only one copy of CUP1, two breaks occur, one centromere-distal and one centromere-proximal to the CUP1 locus. The joining of these broken ends by nonhomologous end-joining results in two products, one with a CUP1 deletion and one with a tandem duplication. An alternative possibility is that the repeats were generated by a single break in the centromere-distal location, followed by a BIR event in which the centromere-proximal site was invaded. Because most BIR events involve either extensive sequence homology (Paques and Haber 1999) or 5−20 bp of microhomology (Payen et al. 2008), and most of the observed breakpoints in our study have very little or no homology, we favor the first alternative.


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)

Generation of a de novo duplication of CUP1 by unequal nonhomologous end-joining. A mechanism for the generation of a two-copy tandem array of CUP1 from a single CUP1 gene (similar to the duplication observed in S288c) is shown. We suggest that, during DNA replication, one fork is broken in the intergenic region between CIC1 and RUF5/CUP1/ARS810. The second fork is broken within RSC30. The nonhomologous end-joining of one broken end to the other (indicated by the dashed line) would produce the duplication. If the other broken ends are also joined, a deletion of RUF5/CUP1/ARS810 would be produced in the sister chromatid.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232551&req=5

fig8: Generation of a de novo duplication of CUP1 by unequal nonhomologous end-joining. A mechanism for the generation of a two-copy tandem array of CUP1 from a single CUP1 gene (similar to the duplication observed in S288c) is shown. We suggest that, during DNA replication, one fork is broken in the intergenic region between CIC1 and RUF5/CUP1/ARS810. The second fork is broken within RSC30. The nonhomologous end-joining of one broken end to the other (indicated by the dashed line) would produce the duplication. If the other broken ends are also joined, a deletion of RUF5/CUP1/ARS810 would be produced in the sister chromatid.
Mentions: All five classes of repeats can be explained by the duplication mechanism shown in Figure 8. We suggest that, during replication of a chromosome with only one copy of CUP1, two breaks occur, one centromere-distal and one centromere-proximal to the CUP1 locus. The joining of these broken ends by nonhomologous end-joining results in two products, one with a CUP1 deletion and one with a tandem duplication. An alternative possibility is that the repeats were generated by a single break in the centromere-distal location, followed by a BIR event in which the centromere-proximal site was invaded. Because most BIR events involve either extensive sequence homology (Paques and Haber 1999) or 5−20 bp of microhomology (Payen et al. 2008), and most of the observed breakpoints in our study have very little or no homology, we favor the first alternative.

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