Hidetoshi Saze

Publications of Hidetoshi Saze

• RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1.

  Authors: Taku Sasaki, Akie Kobayashi, Hidetoshi Saze, Tetsuji Kakutani

  The Plant journal : for cell and molecular biology. 01/2012;

  Methylation of histone H3 lysine 9 (H3K9me) and small RNAs are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked byMethylation of histone H3 lysine 9 (H3K9me) and small RNAs are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. Transposon-specific non-CpG methylation in plants is controlled by small RNAs and H3K9me. Although it is often assumed that small RNA directs H3K9me, interaction between small RNA and H3K9me has not been directly demonstrated in plants. We have previously shown that a mutation in the chromatin remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1) induces a global decrease but a local increase of cytosine methylation and accumulation of small RNA at a locus called BONSAI. Here we show that de novo BONSAI methylation does not depend on RNAi but does depend on H3K9me. In mutants of H3K9 methyltransferase gene KRYPTONITE or the H3K9me-dependent DNA methyltransferase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts (CpG, CpHpG and CpHpH). Furthermore, RNAi mutants showed strong developmental defects when combined with the ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications that may be conserved among diverse eukaryotes.

• Differentiation of epigenetic modifications between transposons and genes.

  Authors: Hidetoshi Saze, Tetsuji Kakutani

  Current opinion in plant biology. 02/2011; 14(1):81-7.

  Transposable elements (TEs) and repeats are methylated and silenced epigenetically in a variety of organisms including plants. Recent results in Arabidopsis suggest that the TE silencing can beTransposable elements (TEs) and repeats are methylated and silenced epigenetically in a variety of organisms including plants. Recent results in Arabidopsis suggest that the TE silencing can be reprogrammed by small RNA during gametogenesis. On the other hand, TE-specific DNA methylation independent of small RNA can be induced by H3K9 methylation through mechanisms conserved between plants and fungi. Methylation of CG sites is found not only in TEs but also in the body of constitutively transcribed genes. Although the function of gene-body methylation is still elusive, the distribution and control of this type of DNA methylation are very similar between plants and animals. Possible interactions of these multiple layers of epigenetic marks and their evolution are discussed.

• Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.

  Authors: Soichi Inagaki, Asuka Miura-Kamio, Yasukazu Nakamura, Falong Lu, Xia Cui, Xiaofeng Cao, Hiroshi Kimura, Hidetoshi Saze, Tetsuji Kakutani

  The EMBO journal. 10/2010; 29(20):3496-506.

  In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical forIn diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical for maintaining genome integrity, mechanisms to exclude H3K9me from active genes remain largely unexplored. Here, we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation). Loss-of-function ibm1 mutation results in ectopic H3K9me and non-CG methylation in thousands of genes. The ibm1-induced genic H3K9me depends on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks--H3K9me and non-CG methylation. Notably, IBM1 enhances loss of H3K9me in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induces ectopic non-CG methylation, which mimics the loss of IBM1 function. We propose that active chromatin is stabilized by an autocatalytic loop of transcription and H3K9 demethylation. This process counteracts a similarly autocatalytic accumulation of silent epigenetic marks, H3K9me and non-CG methylation.

• An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.

  Authors: Asuka Miura, Miyuki Nakamura, Soichi Inagaki, Akie Kobayashi, Hidetoshi Saze, Tetsuji Kakutani

  The EMBO journal. 04/2009;

  Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non-CG sites,Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non-CG sites, whereas the non-CG methylation is rarely found in active genes. Our previous genetic analysis suggested that a jmjC domain-containing protein IBM1 (increase in BONSAI methylation 1) prevents ectopic deposition of non-CG methylation, and this process is necessary for normal Arabidopsis development. Here, we directly determined the genomic targets of IBM1 through high-resolution genome-wide analysis of DNA methylation. The ibm1 mutation induced extensive hyper-methylation in thousands of genes. Transposons were unaffected. Notably, long transcribed genes were most severely affected. Methylation of genes is limited to CG sites in wild type, but CHG sites were also methylated in the ibm1 mutant. The ibm1-induced hyper-methylation did not depend on previously characterized components of the RNAi-based DNA methylation machinery. Our results suggest novel transcription-coupled mechanisms to direct genic methylation not only at CG but also at CHG sites. IBM1 prevents the CHG methylation in genes, but not in transposons.

• Epigenetic memory transmission through mitosis and meiosis in plants.

  Authors: Hidetoshi Saze

  Seminars in cell & developmental biology. 08/2008;

  Gene activities can be regulated by epigenetic modifications of nucleotides and chromatin that are stably propagated through somatic cell divisions and, in some cases, across generations. TheGene activities can be regulated by epigenetic modifications of nucleotides and chromatin that are stably propagated through somatic cell divisions and, in some cases, across generations. The mechanisms that control epigenetic marks have recently been uncovered using model organisms, such as the flowering plant Arabidopsis thaliana. In Arabidopsis, perturbation of epigenetic gene activity often results in heritable developmental phenotypes. Stable, but potentially reversible, changes in epigenetic status can also be sources for phenotypic variations in natural plant populations.

• [Mechanisms to control DNA methylation in Arabidopsis thaliana]

  Authors: Taku Sasaki, Hidetoshi Saze, Tetsuji Kakutani

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 07/2008; 53(7):809-14.

• Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana.

  Authors: Hidetoshi Saze, Akiko Shiraishi, Asuka Miura, Tetsuji Kakutani

  Science (New York, N.Y.). 02/2008; 319(5862):462-5.

  Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosineDifferential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.

• Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1.

  Authors: Hidetoshi Saze, Tetsuji Kakutani

  The EMBO journal. 09/2007; 26(15):3641-52.

  Epigenetically silent transposons and repeats constitute a substantial proportion of eukaryotic genomes, but their impact on cellular gene function remains largely unexplored. In Arabidopsis,Epigenetically silent transposons and repeats constitute a substantial proportion of eukaryotic genomes, but their impact on cellular gene function remains largely unexplored. In Arabidopsis, transposons are silenced by DNA methylation, and this methylation is often abolished by mutations in a chromatin-remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1). The ddm1 mutation induces various types of developmental abnormalities through de-repression of transposons and repeats. Here, we report a novel mechanism for a ddm1-induced syndrome, called bonsai (bns). We identified the gene responsible for the bns phenotypes by genetic linkage analysis and subsequent transcriptional analysis. The bns phenotypes are due to silencing of a putative Anaphase-Promoting Complex (APC) 13 gene. The BNS gene silencing was associated with DNA hypermethylation, which is in contrast to the ddm1-induced hypomethylation in the other genomic regions. This paradoxical BNS hypermethylation was reproducibly induced during self-pollination of the ddm1 mutant, and it was mediated by a long interspersed nuclear element (LINE) retrotransposon flanking the BNS gene. We discuss possible molecular mechanisms and the evolutionary implications of transposon-mediated epigenetic changes in the BNS locus.

• Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats.

  Authors: Yuki Kinoshita, Hidetoshi Saze, Tetsu Kinoshita, Asuka Miura, Wim J J Soppe, Maarten Koornneef, Tetsuji Kakutani

  The Plant journal : for cell and molecular biology. 02/2007; 49(1):38-45.

  A unique feature of late-flowering fwa epigenetic mutations is that the phenotype is caused by ectopic expression of the homeobox gene FWA. During normal development the FWA gene is expressedA unique feature of late-flowering fwa epigenetic mutations is that the phenotype is caused by ectopic expression of the homeobox gene FWA. During normal development the FWA gene is expressed specifically in the endosperm in an imprinted manner. Ectopic FWA expression and disruption of imprinting can be induced in mutants of a CG methyltransferase MET1 (methyltransferase 1) or a chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), suggesting that the proper FWA expression depends on cytosine methylation. However, critical methylated residues controlling FWA silencing are not pinpointed. Nor is it understood how the FWA gene is initially methylated and silenced in wild-type plants. Here we mapped sequences critical for FWA silencing by application of RdDM (RNA-directed DNA methylation) to a ddm1-induced stable fwa epiallele. Transcription of double-stranded RNA corresponding to the tandem direct repeats around the FWA transcription start site induced de novo DNA methylation, transcriptional suppression and phenotypic reversion. The induced changes were heritable even without the transgene, which correlates with inheritance of CG methylation in the direct repeats. The newly silenced FWA allele was transcribed in an endosperm-specific and imprinted manner, as is the case for the wild-type FWA gene. The results indicate that methylation of the direct repeats, which presumably originated from a short interspersed nuclear element (SINE), is sufficient to induce proper epigenetic control of the FWA gene.

• [Epigenetics in Arabidopsis thaliana]

  Authors: Hidetoshi Saze, Tetsuji Kakutani

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 05/2004; 49(5):634-41.

• Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin.

  Authors: Muhammad Tariq, Hidetoshi Saze, Aline V Probst, Jacek Lichota, Yoshiki Habu, Jerzy Paszkowski

  Proceedings of the National Academy of Sciences of the United States of America. 08/2003; 100(15):8823-7.

  In mammals and plants, formation of heterochromatin is associated with hypermethylation of DNA at CpG sites and histone H3 methylation at lysine 9. Previous studies have revealed that maintenance ofIn mammals and plants, formation of heterochromatin is associated with hypermethylation of DNA at CpG sites and histone H3 methylation at lysine 9. Previous studies have revealed that maintenance of DNA methylation in Neurospora and Arabidopsis requires histone H3 methylation. A feedback loop from DNA methylation to histone methylation, however, is less understood. Its recent examination in Arabidopsis with a partial loss of function in DNA methyltransferase 1 (responsible for maintenance of CpG methylation) yielded conflicting results. Here we report that complete removal of CpG methylation in an Arabidopsis mutant null for DNA maintenance methyltransferase results in a clear loss of histone H3 methylation at lysine 9 in heterochromatin and also at heterochromatic loci that remain transcriptionally silent. Surprisingly, these dramatic alterations are not reflected in heterochromatin relaxation.

• Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis.

  Authors: Hidetoshi Saze, Ortrun Mittelsten Scheid, Jerzy Paszkowski

  Nature genetics. 06/2003; 34(1):65-9.

  In mammals, the DNA methyltransferase 1 (Dnmt1) faithfully copies the pattern of cytosine methylation at CpG sites to the newly synthesized strand, and this is essential for epigenetic inheritance.In mammals, the DNA methyltransferase 1 (Dnmt1) faithfully copies the pattern of cytosine methylation at CpG sites to the newly synthesized strand, and this is essential for epigenetic inheritance. In Arabidopsis thaliana, several DNA methyltransferases or chromatin modifiers coupled to methylation changes have been characterized, and mutations that cause loss of their function are recessive. This is surprising because plant gametogenesis includes postmeiotic DNA replication in haploid nuclei before fertilization. Therefore, the recessive character of the mutations excludes the affected components from a regulatory role in postmeiotic maintenance or modification of epigenetic states. Here we show, however, that depletion of A. thaliana MET1, a homolog of mammalian Dnmt1 (ref. 8), results in immense epigenetic diversification of gametes. This diversity seems to be a consequence of passive postmeiotic demethylation, leading to gametes with fully demethylated and hemidemethylated DNA, followed by remethylation of hemimethylated templates once MET1 is again supplied in a zygote.

• Negative regulation of DNA methylation in plants.

  Authors: Hidetoshi Saze, Taku Sasaki, Tetsuji Kakutani

  Epigenetics : official journal of the DNA Methylation Society. 3(3):122-4.

  Cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene function. In plants, DNA methylation is regulated by DNA methyltransferases, chromatinCytosine methylation of repeats and genes is important for coordination of genome stability and proper gene function. In plants, DNA methylation is regulated by DNA methyltransferases, chromatin remodeling factors and RNAi machinery. Ectopic DNA hypermethylation at genes causes transcriptional repression and silencing, and the methylation patterns often become heritable over generations. DNA methylation is antagonized by the DNA demethylation enzymes. Recently, we identified a novel jmjC-domain containing gene IBM1 (increase in bonsai methylation1) that also negatively regulates DNA methylation in Arabidopsis. The ibm1 plants show a variety of developmental phenotypes. IBM1 prevents ectopic accumulation of DNA methylation at the BNS genic region, likely through removal of heterochromatic H3K9 methylation mark. DNA and histone demethylation pathways are important for genome-wide patterning of DNA methylation and for epigenetic regulation of plant development.