Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

Abstract

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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Primary accessions

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.

References

  1. 1

    Arias, E. E. & Walter, J. C. Strength in numbers: preventing rereplication via multiple mechanisms in eukaryotic cells. Genes Dev. 21, 497–518 (2007)

    CAS  Article  Google Scholar 

  2. 2

    Jacob, Y. et al. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nature Struct. Mol. Biol. 16, 763–768 (2009)

    CAS  Article  Google Scholar 

  3. 3

    Raynaud, C. et al. Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis. Plant J. 47, 395–407 (2006)

    CAS  Article  Google Scholar 

  4. 4

    Jackson, J. P., Lindroth, A. M., Cao, X. & Jacobsen, S. E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556–560 (2002)

    ADS  CAS  Article  Google Scholar 

  5. 5

    Malagnac, F., Bartee, L. & Bender, J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J. 21, 6842–6852 (2002)

    CAS  Article  Google Scholar 

  6. 6

    Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M. & Jacobsen, S. E. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS ONE 3, e3156 (2008)

    ADS  Article  Google Scholar 

  7. 7

    Obayashi, T., Hayashi, S., Saeki, M., Ohta, H. & Kinoshita, K. ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res. 37, D987–D991 (2009)

    CAS  Article  Google Scholar 

  8. 8

    Moldovan, G. L., Pfander, B. & Jentsch, S. PCNA, the maestro of the replication fork. Cell 129, 665–679 (2007)

    CAS  Article  Google Scholar 

  9. 9

    Galbraith, D. W., Harkins, K. R. & Knapp, S. Systemic endopolyploidy in Arabidopsis thaliana. Plant Physiol. 96, 985–989 (1991)

    CAS  Article  Google Scholar 

  10. 10

    Caro, E., Desvoyes, B., Ramirez-Parra, E., Sanchez, M. P. & Gutierrez, C. Endoreduplication control during plant development. SEB Exp. Biol. Ser. 59, 167–187 (2008)

    CAS  PubMed  Google Scholar 

  11. 11

    Jeddeloh, J. A., Stokes, T. L. & Richards, E. J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nature Genet. 22, 94–97 (1999)

    CAS  Article  Google Scholar 

  12. 12

    Fransz, P., ten Hoopen, R. & Tessadori, F. Composition and formation of heterochromatin in Arabidopsis thaliana. Chromosome Res. 14, 71–82 (2006)

    CAS  Article  Google Scholar 

  13. 13

    Soppe, W. J. et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21, 6549–6559 (2002)

    CAS  Article  Google Scholar 

  14. 14

    Pauler, F. M. et al. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res. 19, 221–233 (2009)

    CAS  Article  Google Scholar 

  15. 15

    Gomez, M. Controlled rereplication at DNA replication origins. Cell Cycle 7, 1313–1314 (2008)

    CAS  Article  Google Scholar 

  16. 16

    Fuchs, J., Demidov, D., Houben, A. & Schubert, I. Chromosomal histone modification patterns—from conservation to diversity. Trends Plant Sci. 11, 199–208 (2006)

    CAS  Article  Google Scholar 

  17. 17

    Lindroth, A. M. et al. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23, 4146–4155 (2004)

    Article  Google Scholar 

  18. 18

    Mathieu, O., Probst, A. V. & Paszkowski, J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J. 24, 2783–2791 (2005)

    CAS  Article  Google Scholar 

  19. 19

    Musselman, C. A. & Kutateladze, T. G. PHD fingers: epigenetic effectors and potential drug targets. Mol. Interv. 9, 314–323 (2009)

    CAS  Article  Google Scholar 

  20. 20

    Zhang, X., Bernatavichute, Y. V., Cokus, S., Pellegrini, M. & Jacobsen, S. E. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 10, R62 (2009)

    Article  Google Scholar 

  21. 21

    Jiang, H. & Wong, W. H. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24, 2395–2396 (2008)

    CAS  Article  Google Scholar 

  22. 22

    Davidson, I. F., Li, A. & Blow, J. J. Deregulated replication licensing causes DNA fragmentation consistent with head-to-tail fork collision. Mol. Cell 24, 433–443 (2006)

    CAS  Article  Google Scholar 

  23. 23

    Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926–1928 (1993)

    ADS  CAS  Article  Google Scholar 

  24. 24

    Lan, F. et al. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448, 718–722 (2007)

    ADS  CAS  Article  Google Scholar 

  25. 25

    Dillon, S. C., Zhang, X., Trievel, R. C. & Cheng, X. The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol. 6, 227 (2005)

    Article  Google Scholar 

  26. 26

    Joshi, P. et al. Dominant alleles identify SET domain residues required for histone methyltransferase of Polycomb repressive complex 2. J. Biol. Chem. 283, 27757–27766 (2008)

    CAS  Article  Google Scholar 

  27. 27

    Earley, K. W. et al. Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 45, 616–629 (2006)

    CAS  Article  Google Scholar 

  28. 28

    Curtis, M. D. & Grossniklaus, U. A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta[w]. Plant Physiol. 133, 462–469 (2003)

    CAS  Article  Google Scholar 

  29. 29

    Shi, X. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442, 96 (2006)

    ADS  CAS  Article  Google Scholar 

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Acknowledgements

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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Jacob, Y., Stroud, H., LeBlanc, C. et al. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 466, 987–991 (2010). https://doi.org/10.1038/nature09290

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