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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Wyman, C. & Kanaar, R. DNA double-strand break repair: all’s well that ends well. Annu. Rev. Genet. 40, 363–383 (2006).
Agarwal, S., Tafel, A. A. & Kanaar, R. DNA double-strand break repair and chromosome translocations. DNA Repair (Amst) 5, 1075–1081 (2006).
Rassool, F. V. DNA double strand breaks (DSB) and non-homologous end joining (NHEJ) pathways in human leukemia. Cancer Lett. 193, 1–9 (2003).
Thorslund, T. & West, S. C. BRCA2: a universal recombinase regulator. Oncogene 26, 7720–7730 (2007).
Barzel, A. & Kupiec, M. Finding a match: how do homologous sequences get together for recombination? Nat. Rev. Genet. 9, 27–37 (2008).
Soutoglou, E. & Misteli, T. Mobility and immobility of chromatin in transcription and genome stability. Curr. Opin. Genet Dev. 17, 435–442 (2007).
Soutoglou, E. & Misteli, T. On the contribution of spatial genome organization to cancerous chromosome translocations. J. Natl Cancer Inst. Monogr. 39, 16–19 (2008).
Meister, P., Gehlen, L. R., Varela, E., Kalck, V. & Gasser, S. M. Visualizing yeast chromosomes and nuclear architecture. Methods Enzymol. 470, 535–567 (2010).
Zimmer, C. & Fabre, E. Principles of chromosomal organization: lessons from yeast. J. Cell Biol. 192, 723–733 (2011).
Heun, P., Laroche, T., Shimada, K., Furrer, P. & Gasser, S. M. Chromosome dynamics in the yeast interphase nucleus. Science 294, 2181–2186 (2001).
Marshall, W. F. et al. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7, 930–939 (1997).
Courty, S. et al. Tracking individual proteins in living cells using single quantum dot imaging. Methods Enzymol. 414, 211–228 (2006).
Nagai, S. et al. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science 322, 597–602 (2008).
Oza, P., Jaspersen, S. L., Miele, A., Dekker, J. & Peterson, C. L. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev. 23, 912–927 (2009).
Lisby, M., Mortensen, U. H. & Rothstein, R. Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nat. Cell Biol. 5, 572–577 (2003).
Robinett, C. C. et al. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J. Cell Biol. 135, 1685–1700 (1996).
Burgess, S. M., Kleckner, N. & Weiner, B. M. Somatic pairing of homologs in budding yeast: existence and modulation. Genes Dev. 13, 1627–1641 (1999).
Gasser, S. M. Visualizing chromatin dynamics in interphase nuclei. Science 296, 1412–1416 (2002).
Hajjoul, H., Kocanova, S., Lassadi, I., Bystricky, K. & Bancaud, A. Lab-on-Chip for fast 3D particle tracking in living cells. Lab Chip 9, 3054–3058 (2009).
Ma, W., Resnick, M. A. & Gordenin, D. A. Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis. Nucleic Acids Res. 36, 1836–1846 (2008).
Chiolo, I. et al. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 144, 732–744 (2011).
Dion, V., Klack, V., Horigome, C., Towbin, B. D. & Gasser, S. Increased mobility of double-strand breaks requires Mec1, Rad9 and the recombination machinery. Nat. Cell Biol.http://dx.doi.org/10.1038/ncb2465 (2012).
Lisby, M., Barlow, J. H., Burgess, R. C. & Rothstein, R. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118, 699–713 (2004).
Houston, P. L. & Broach, J. R. The dynamics of homologous pairing during mating type interconversion in budding yeast. PLoS Genet. 2, e98 (2006).
Aten, J. A. et al. Dynamics of DNA double-strand breaks revealed by clustering of damaged chromosome domains. Science 303, 92–95 (2004).
Dimitrova, N., Chen, Y. C., Spector, D. L. & de Lange, T. 53BP1 promotes non-homologous end joining of telomeres by increasing chromatin mobility. Nature 456, 524–528 (2008).
Difilippantonio, S. et al. 53BP1 facilitates long-range DNA end-joining during V(D)J recombination. Nature 456, 529–533 (2008).
Benichou, O. & Voituriez, R. Optimization of the residence time of a Brownian particle in a spherical subdomain. J. Chem. Phys. 131, 181104 (2009).
Dorfman, K. D., Fulconis, R., Dutreix, M. & Viovy, J. L. Model of RecA-mediated homologous recognition. Phys. Rev. Lett. 93, 268102 (2004).
Savir, Y. & Tlusty, T. RecA-mediated homology search as a nearly optimal signal detection system. Mol. Cell 40, 388–396 (2010).
Dutreix, M., Fulconis, R. & Viovy, J. L. The search for homology: a paradigm for molecular interactions? Complexus 1, 89–99 (2003).
Shiloh, Y. The ATM-mediated DNA-damage response: taking shape. Trends Biochem. Sci. 31, 402–410 (2006).
Thomas, B. J. & Rothstein, R. Elevated recombination rates in transcriptionally active DNA. Cell 56, 619–630 (1989).
Zou, H. & Rothstein, R. Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism. Cell 90, 87–96 (1997).
Herskowitz, I. & Jensen, R. E. Putting the HO gene to work: practical uses for mating-type switching. Methods Enzymol. 194, 132–146 (1991).
Berger, A. B. et al. High-resolution statistical mapping reveals gene territories in live yeast. Nat. Methods 5, 1031–1037 (2008).
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.).
Author information
Authors and Affiliations
Contributions
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.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Information
Supplementary Information (PDF 578 kb)
Supplementary Table 1
Supplementary Information (XLS 25 kb)
Supplementary Table 2
Supplementary Information (XLS 27 kb)
Supplementary Movie 1
Supplementary Information (MOV 99 kb)
Supplementary Movie 2
Supplementary Information (MOV 15 kb)
Supplementary Movie 3
Supplementary Information (MOV 19 kb)
Supplementary Movie 4
Supplementary Information (MOV 150 kb)
Supplementary Movie 5
Supplementary Information (MOV 22 kb)
Supplementary Movie 6
Supplementary Information (MOV 35 kb)
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ncb2472
This article is cited by
-
Distinct characteristics of the DNA damage response in mammalian oocytes
Experimental & Molecular Medicine (2024)
-
In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search
Nature Structural & Molecular Biology (2023)
-
Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization
Nature Structural & Molecular Biology (2023)
-
Actin up: shifting chromosomes toward repair, but also translocations
Nature Structural & Molecular Biology (2023)
-
Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions
Stress Biology (2021)