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Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks

Nature Structural & Molecular Biology volume 18, pages 395–400 (2011)Cite this article

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Abstract

Genome integrity requires faithful chromosome duplication. Origins of replication, the genomic sites at which DNA replication initiates, are scattered throughout the genome. Their mapping at a genomic scale in multicellular organisms has been challenging. In this study we profiled origins in Arabidopsis thaliana by high-throughput sequencing of newly synthesized DNA and identified ~1,500 putative origins genome-wide. This was supported by chromatin immunoprecipitation and microarray (ChIP-chip) experiments to identify ORC1- and CDC6-binding sites. We validated origin activity independently by measuring the abundance of nascent DNA strands. The midpoints of most A. thaliana origin regions are preferentially located within the 5′ half of genes, enriched in G+C, histone H2A.Z, H3K4me2, H3K4me3 and H4K5ac, and depleted in H3K4me1 and H3K9me2. Our data help clarify the epigenetic specification of DNA replication origins in A. thaliana and have implications for other eukaryotes.

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Figure 1: Identification of DNA replication origins in the A. thaliana genome.
Figure 2: DNA replication origin activity determined by nascent DNA strand abundance.
Figure 3: Genomic location of A. thaliana replication origins.
Figure 4: Relationship of A. thaliana replication origins to CG methylation and histone H2A.Z.
Figure 5: Histone modification landscape around replication origins.

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Acknowledgements

We thank E. Martinez-Salas, J.A. Tercero and E. Caro for comments and discussions, S. Diaz-Triviño and P. Hernandez for initial efforts in origin mapping, and M. Gomez and J. Sequeira-Mendes for advice with the purification and analysis of nascent DNA strands. The technical help of V. Mora-Gil is deeply acknowledged. M.P.S. and C.C. are recipients of JAE-Doc contracts from CSIC. S.F. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation. This research has been supported by grants BFU2006-5662, BFU2009-9783 and CSD2007-00057-B (Spain Ministry of Science and Education) and P2006/GEN0191 (Comunidad de Madrid) to C.G., by an institutional grant from Fundación Ramón Areces to C.B.M., by grant GM60398 (US National Institutes of Health) to S.E.J., by grant 0960425 (US National Science Foundation) to X.Z. and by grants BIO2004-02502, BIO2007-66935, GEN2003-20218-C02-02 and CSD2007-00057-B (Spain Ministry of Science and Innovation) and GR/SAL/0674/2004 (Comunidad de Madrid) to R.S. S.E.J. is an investigator of the Howard Hughes Medical Institute.

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Author notes

  1. Maria de la Paz Sanchez

    Present address: Present address: Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico DF, Mexico.,

  2. Celina Costas, Maria de la Paz Sanchez and Hume Stroud: These authors contributed equally to this work.

Authors and Affiliations

  1. Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad autónoma de Madrid (UAM), Madrid, Spain

    Celina Costas, Maria de la Paz Sanchez & Crisanto Gutierrez

  2. Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA

    Hume Stroud & Steven E Jacobsen

  3. Department of Plant Biology, University of Georgia, Athens, Georgia, USA

    Yanchun Yu & Xiaoyu Zhang

  4. Centro Nacional de Biotecnología, CSIC, Madrid, Spain

    Juan Carlos Oliveros, Alberto Benguria, Irene López-Vidriero & Roberto Solano

  5. Howard Hughes Medical Institute, University of California, Los Angeles, California, USA

    Suhua Feng & Steven E Jacobsen

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Contributions

C.C., M.P.S., Y.Y., S.F., A.B. and I.L.-V. carried out experiments. H.S., J.C.O., C.C., M.P.S., X.Z. and R.S. analyzed data. C.G. and S.E.J. prepared the manuscript.

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Correspondence to Steven E Jacobsen or Crisanto Gutierrez.

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Supplementary Figures 1–7 and Supplementary Table 2 (PDF 752 kb)

Supplementary Table 1

Putative Arabidopsis DNA replication origins (originome) (TXT 428 kb)

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Costas, C., de la Paz Sanchez, M., Stroud, H. et al. Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks. Nat Struct Mol Biol 18, 395–400 (2011). https://doi.org/10.1038/nsmb.1988

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