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ATP-dependent chromatin remodeling shapes the DNA replication landscape

Nature Structural & Molecular Biology volume 15, pages 477–484 (2008)Cite this article

Abstract

The eukaryotic DNA replication machinery must traverse every nucleosome in the genome during S phase. As nucleosomes are generally inhibitory to DNA-dependent processes, chromatin structure must undergo extensive reorganization to facilitate DNA synthesis. However, the identity of chromatin-remodeling factors involved in replication and how they affect DNA synthesis is largely unknown. Here we show that two highly conserved ATP-dependent chromatin-remodeling complexes in Saccharomyces cerevisiae, Isw2 and Ino80, function in parallel to promote replication fork progression. As a result, Isw2 and Ino80 have especially important roles for replication of late-replicating regions during periods of replication stress. Both Isw2 and Ino80 complexes are enriched at sites of replication, suggesting that these complexes act directly to promote fork progression. These findings identify ATP-dependent chromatin-remodeling complexes that promote DNA replication and define a specific stage of replication that requires remodeling for normal function.

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Figure 1: MMS sensitivity of isw2 nhp10 mutants is due to a prolonged S phase.
Figure 2: Isw2 and Ino80 complexes are required for efficient replication of late-replicating regions in the presence of MMS.
Figure 3: Replication fork progression is slowed in isw2 nhp10 mutants.
Figure 4: Isw2 and Ino80 may directly facilitate DNA replication.
Figure 5: Isw2 and Ino80 promote replication in the absence of MMS.

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Acknowledgements

We thank G.M. Alvino, S. Biggins, B.J. Brewer, D. Collingwood, H.S. Malik, M.K. Raghuraman and members of the Tsukiyama laboratory for critical reading of the manuscript; J.F.X. Diffley (Cancer Research UK) for the YJT80 strain; members of the Biggins and Brewer-Raghuraman laboratories for helpful discussions; D. Collingwood for help with analysis of replication data; H.S. Malik for the manuscript title suggestion; C.L. Peterson for sharing data before publication; and G.M. Alvino for a DNA-labeling protocol for microarrays, technical advice on density transfer experiments and help with replication data analysis. This work was supported by grants to T.T. from the US National Institutes of Health (NIH) and the Leukemia and Lymphoma Society. J.A.V. and T.J.K. were supported in part by training grants from the NIH.

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Authors and Affiliations

  1. Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA, and Molecular and Cellular Biology Program, University of Washington and Fred Hutchinson Cancer Research Center, Box 357275, Seattle, Washington 98195, USA.,

    Jack A Vincent, Tracey J Kwong & Toshio Tsukiyama

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  1. Jack A Vincent
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Contributions

J.A.V. designed and conducted the drug sensitivity, FACS, DNA microarray and DNA replication experiments, and wrote the manuscript; T.J.K. designed and conducted the ChIP experiments; T.T. supervised the project and contributed as the senior author. All authors contributed to the preparation of the manuscript.

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Correspondence to Toshio Tsukiyama.

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Vincent, J., Kwong, T. & Tsukiyama, T. ATP-dependent chromatin remodeling shapes the DNA replication landscape. Nat Struct Mol Biol 15, 477–484 (2008). https://doi.org/10.1038/nsmb.1419

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