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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Arias, E. E. & Walter, J. C. Strength in numbers: preventing rereplication via multiple mechanisms in eukaryotic cells. Genes Dev. 21, 497–518 (2007)
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)
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)
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)
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)
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)
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)
Moldovan, G. L., Pfander, B. & Jentsch, S. PCNA, the maestro of the replication fork. Cell 129, 665–679 (2007)
Galbraith, D. W., Harkins, K. R. & Knapp, S. Systemic endopolyploidy in Arabidopsis thaliana. Plant Physiol. 96, 985–989 (1991)
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)
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)
Fransz, P., ten Hoopen, R. & Tessadori, F. Composition and formation of heterochromatin in Arabidopsis thaliana. Chromosome Res. 14, 71–82 (2006)
Soppe, W. J. et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21, 6549–6559 (2002)
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)
Gomez, M. Controlled rereplication at DNA replication origins. Cell Cycle 7, 1313–1314 (2008)
Fuchs, J., Demidov, D., Houben, A. & Schubert, I. Chromosomal histone modification patterns—from conservation to diversity. Trends Plant Sci. 11, 199–208 (2006)
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)
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)
Musselman, C. A. & Kutateladze, T. G. PHD fingers: epigenetic effectors and potential drug targets. Mol. Interv. 9, 314–323 (2009)
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)
Jiang, H. & Wong, W. H. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24, 2395–2396 (2008)
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)
Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926–1928 (1993)
Lan, F. et al. Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448, 718–722 (2007)
Dillon, S. C., Zhang, X., Trievel, R. C. & Cheng, X. The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol. 6, 227 (2005)
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)
Earley, K. W. et al. Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 45, 616–629 (2006)
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)
Shi, X. et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442, 96 (2006)
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.
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). https://doi.org/10.1038/nature09290
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