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Increased chromosome mobility facilitates homology search during recombination

Abstract

Homologous recombination, an essential process for preserving genomic integrity, uses intact homologous sequences to repair broken chromosomes. To explore the mechanism of homologous pairing in vivo, we tagged two homologous loci in diploid yeast Saccharomyces cerevisiae cells and investigated their dynamic organization in the absence and presence of DNA damage. When neither locus is damaged, homologous loci occupy largely separate regions, exploring only 2.7% of the nuclear volume. Following the induction of a double-strand break, homologous loci co-localize ten times more often. The mobility of the cut chromosome markedly increases, allowing it to explore a nuclear volume that is more than ten times larger. Interestingly, the mobility of uncut chromosomes also increases, allowing them to explore a four times larger volume. We propose a model for homology search in which increased chromosome mobility facilitates homologous pairing. Finally, we find that the increase in DNA dynamics is dependent on early steps of homologous recombination.

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Figure 1: Description of the strain used to study chromosome dynamics.
Figure 2: Characterization of the dynamics of homologous loci in the absence of DSBs.
Figure 3: Characterization of I-SceI cutting and repair product formation in wild-type cells.
Figure 4: Characterization of the pairing and dynamics of homologous loci in the presence of a single DSB.
Figure 5: The dynamics of unbroken non-homologous chromosomes is also increased in the presence of one or two DSBs.
Figure 6: Different levels of γ-irradiation also increase chromosome dynamics.
Figure 7: Pairing and dynamics of homologous loci in rad51Δ and sae2Δ cells.

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Acknowledgements

We would like to thank M. Lisby and X. Darzacq for fruitful comments about this work as well V. Dion and S. Gasser for sharing results before publication. The LacIR197K mutant protein was engineered by C. Muller. We also thank L. Symington and G. Mazon for help in performing the genomic blots. Thanks are also due to L. Symington, I. Izeddin, V. Recamier, A. Gupta, P. Thorpe, M. Chang, R. Reid, N. Mandriota and K. Bernstein for helpful discussions and comments on the manuscript. This work was financially supported by an EMBO Long-Term fellowship (J.M-H.), a Marie Curie International Outgoing Fellowship (J.M-H.), the Bettencourt Foundation (J.M-H.), a postdoctoral award from the Philippe Foundation (J.M-H.) and a grant from the NIH (GM67055 to R.R.).

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J.M-H. and R.R. contributed to the project planning, data interpretation and writing. J.M-H. contributed to the experimental work and the data analyses.

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Correspondence to Rodney Rothstein.

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The authors declare no competing financial interests.

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Miné-Hattab, J., Rothstein, R. Increased chromosome mobility facilitates homology search during recombination. Nat Cell Biol 14, 510–517 (2012). https://doi.org/10.1038/ncb2472

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