Article | Published:

Intrinsic coupling of lagging-strand synthesis to chromatin assembly

Nature volume 483, pages 434438 (22 March 2012) | Download Citation

Abstract

Fifty per cent of the genome is discontinuously replicated on the lagging strand as Okazaki fragments. Eukaryotic Okazaki fragments remain poorly characterized and, because nucleosomes are rapidly deposited on nascent DNA, Okazaki fragment processing and nucleosome assembly potentially affect one another. Here we show that ligation-competent Okazaki fragments in Saccharomyces cerevisiae are sized according to the nucleosome repeat. Using deep sequencing, we demonstrate that ligation junctions preferentially occur near nucleosome midpoints rather than in internucleosomal linker regions. Disrupting chromatin assembly or lagging-strand polymerase processivity affects both the size and the distribution of Okazaki fragments, suggesting a role for nascent chromatin, assembled immediately after the passage of the replication fork, in the termination of Okazaki fragment synthesis. Our studies represent the first high-resolution analysis—to our knowledge—of eukaryotic Okazaki fragments in vivo, and reveal the interconnection between lagging-strand synthesis and chromatin assembly.

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Primary accessions

Gene Expression Omnibus

Data deposits

Raw sequencing data and processed data are available at theGene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33786) under accession number 33786.

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Acknowledgements

We thank S. McGuffee for assistance with data processing; S. Keeney, K. Marians, D. Remus, T. Tsukiyama, members of the Molecular Biology Program and Whitehouse laboratory for discussions and comments on the manuscript. This work was supported by a Louis V. Gerstner Jr Young Investigator Award and an Alfred Bressler Scholars Endowment Award to I.W. D.J.S. is an HHMI fellow of the Damon Runyon Cancer Research Foundation (DRG-#2046-10).

Author information

Affiliations

  1. Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA

    • Duncan J. Smith
    •  & Iestyn Whitehouse

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Contributions

D.J.S. and I.W. designed experiments; D.J.S. performed experiments and analysed data; D.J.S. and I.W. interpreted results; the manuscript was drafted by D.J.S. and edited by D.J.S. and I.W.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Iestyn Whitehouse.

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    Supplementary Information

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https://doi.org/10.1038/nature10895

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