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Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

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Multiple pathways prevent DNA replication from occurring more than once per cell cycle1. These pathways block re-replication by strictly controlling the activity of pre-replication complexes, which assemble at specific sites in the genome called origins. Here we show that mutations in the homologous histone 3 lysine 27 (H3K27) monomethyltransferases, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, lead to re-replication of specific genomic locations. Most of these locations correspond to transposons and other repetitive and silent elements of the Arabidopsis genome. These sites also correspond to high levels of H3K27 monomethylation, and mutation of the catalytic SET domain is sufficient to cause the re-replication defect. Mutation of ATXR5 and ATXR6 also causes upregulation of transposon expression and has pleiotropic effects on plant development. These results uncover a novel pathway that prevents over-replication of heterochromatin in Arabidopsis.

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Figure 1: Heterochromatic DNA is over-produced in atxr5 atxr6 mutants.
Figure 2: Increased heterochromatic DNA in atxr5 atxr6 mutants is consistent with re-replication of chromatin.
Figure 3: Genome-wide mapping of H3K27me1 and anticorrelation with H3K4 methylation.
Figure 4: Functional PHD and SET domains and the PIP motif are required for the regulation of DNA replication by ATXR6.

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Gene Expression Omnibus

Data deposits

Sequencing files have been deposited at GEO (accession codes GSE22411 and GSE21673).

Change history

  • 19 August 2010

    Author Luting Zhuo's family name was corrected for the print issue.


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We thank G. Lambert and D. Galbraith for assistance with flow cytometry; Y. Bernatavichute for assistance with ChIP experiments; and M. Pellegrini and S. Cokus for advice on data analyses. Y.J. was supported by a fellowship from Le Fonds Québécois de la Recherche sur la Nature et les Technologies (FQRNT). S.F. is a Howard Hughes Medical Institute Fellow of the Life Science Research Foundation. Research in the Michaels’ laboratory was supported by grants from the National Institutes of Health (GM075060), the Indiana METACyt Initiative of Indiana University, and the Lilly Endowment, Inc. C.G. was supported by grants from the Spanish Ministry of Science and Innovation (BFU2009-9783 and CSD2007-57B). S.E.J. is an investigator of the Howard Hughes Medical Institute.

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S.D.M., S.E.J. and C.G. directed the research. Y.J., H.S., C.L., S.F., L.Z., E.C. and C.H. performed experiments. H.S. analysed data. H.S., Y.J., S.E.J. and S.D.M. prepared the manuscript.

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Correspondence to Scott D. Michaels or Steven E. Jacobsen.

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The authors declare no competing financial interests.

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Jacob, Y., Stroud, H., LeBlanc, C. et al. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 466, 987–991 (2010).

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