Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

Multiple pathways prevent DNA replication from occurring more than once per cell cycle. 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.

[1]  Anjanabha Saha,et al.  ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression , 2006, Nature.

[2]  U. Grossniklaus,et al.  A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta[w] , 2003, Plant Physiology.

[3]  M. Pellegrini,et al.  Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana , 2008, PloS one.

[4]  J. Jeddeloh,et al.  Maintenance of genomic methylation requires a SWI2/SNF2-like protein , 1999, Nature Genetics.

[5]  J. P. Jackson,et al.  Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase , 2002, Nature.

[6]  S. Jacobsen,et al.  DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis , 2002, The EMBO journal.

[7]  D. Galbraith,et al.  Systemic Endopolyploidy in Arabidopsis thaliana. , 1991, Plant physiology.

[8]  C. Gutiérrez,et al.  Endoreduplication control during plant development. , 2008, SEB experimental biology series.

[9]  Andreas Houben,et al.  Chromosomal histone modification patterns--from conservation to diversity. , 2006, Trends in plant science.

[10]  M. Gomez Controlled rereplication at DNA replication origins , 2008, Cell cycle.

[11]  A. Probst,et al.  Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis , 2005, The EMBO journal.

[12]  Wing Hung Wong,et al.  SeqMap: mapping massive amount of oligonucleotides to the genome , 2008, Bioinform..

[13]  R. Schekman,et al.  GTP/GDP exchange by Sec12p enables COPII vesicle bud formation on synthetic liposomes , 2004, The EMBO journal.

[14]  Xing Zhang,et al.  The SET-domain protein superfamily: protein lysine methyltransferases , 2005, Genome Biology.

[15]  J. Simon,et al.  Dominant Alleles Identify SET Domain Residues Required for Histone Methyltransferase of Polycomb Repressive Complex 2* , 2008, Journal of Biological Chemistry.

[16]  J. Walter,et al.  Strength in numbers: preventing rereplication via multiple mechanisms in eukaryotic cells. , 2007, Genes & development.

[17]  R. Martienssen,et al.  Arabidopsis thaliana DNA methylation mutants. , 1993, Science.

[18]  Rosangela Sozzani,et al.  Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis. , 2006, The Plant journal : for cell and molecular biology.

[19]  Kengo Kinoshita,et al.  ATTED-II provides coexpressed gene networks for Arabidopsis , 2008, Nucleic Acids Res..

[20]  J. Blow,et al.  Deregulated Replication Licensing Causes DNA Fragmentation Consistent with Head-to-Tail Fork Collision , 2006, Molecular cell.

[21]  M. Pellegrini,et al.  Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana , 2009, Genome Biology.

[22]  M. Pellegrini,et al.  ATXR5 and ATXR6 are novel H3K27 monomethyltransferases required for chromatin structure and gene silencing , 2009, Nature Structural &Molecular Biology.

[23]  J. Bender,et al.  An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation , 2002, The EMBO journal.

[24]  C. Musselman,et al.  PHD fingers: epigenetic effectors and potential drug targets. , 2009, Molecular interventions.

[25]  T. Jenuwein,et al.  Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3 , 2004, The EMBO journal.

[26]  R. T. Hoopen,et al.  Composition and formation of heterochromatin in Arabidopsis thaliana , 2006, Chromosome Research.

[27]  C. Pikaard,et al.  Gateway-compatible vectors for plant functional genomics and proteomics. , 2006, The Plant journal : for cell and molecular biology.

[28]  A. Aszódi,et al.  H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. , 2009, Genome research.

[29]  Yang Shi,et al.  Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression , 2007, Nature.

[30]  S. Jentsch,et al.  PCNA, the Maestro of the Replication Fork , 2007, Cell.