Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Soichi Inagaki
PROVIDER: E-GEOD-23030 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.
Inagaki Soichi S Miura-Kamio Asuka A Nakamura Yasukazu Y Lu Falong F Cui Xia X Cao Xiaofeng X Kimura Hiroshi H Saze Hidetoshi H Kakutani Tetsuji T
The EMBO journal 20100910 20
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 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 ...[more]
Similar Datasets
Project description:In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Despites the conservation and importance in the genome integrity, mechanisms to exclude H3K9m from active genes remained 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 caused ectopic H3K9me in thousands of genes, which accompanies genic DNA methylation at non-CG sites. The ibm1-induced genic H3K9me depended on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks – H3K9me and non-CG methylation. Notably, IBM1 enhanced loss of H3K9m in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induced ectopic non-CG methylation, mimicking the loss of IBM1 function. We propose that active chromatin is stabilized by the autocatalytic loop of transcription and H3K9 demethylation. This process counteracts accumulation of silent epigenetic marks, H3K9me and non-CG methylation, which is also autocatalytic. Leaves of 4-week-old plants were fixed as described previously (Saze et al, 2008). Chromatin immunoprecipitation (ChIP) was performed as described previously (Kimura et al, 2008), using antibody against H3K9me2 (CMA307, Kimura et al, 2008, PMID: 18227620). Non-immunoprecipitated DNA (input DNA) and ChIP samples were amplified, labeled, and hybridized to microarray according to the manufacturer’s instruction (Protocols for Chromatin Immunoprecipitation and Amplification, NimbleGen). Input DNA and ChIP DNA were differentially labeled with Cy3 and Cy5, respectively, and competitively hybridized to a microarray chip. We used NimbleGen 2.1M HD2 array covering entire genome of A. thaliana.
2010-09-21 | E-GEOD-22953 | biostudies-arrayexpress
Project description:Heterochromatin constitutes a fundamental aspect of genomes that is crucial for maintaining genome stability. In flowering plants, maintenance of heterochromatin relies on a positive feedback loop involving the histone 3 lysine nine methyltransferase (H3K9), KRYPTONITE (KYP), and the DNA methyltransferase, CHROMOMETHYLASE3 (CMT3). An H3K9 demethylase, INCREASED IN BONSAI METHYLATION 1 (IBM1), has evolved to modulate the activity of KYP-CMT3 within transcribed genes. The absence of IBM1 activity results in aberrant methylation of gene bodies, which is deleterious. This study demonstrates extensive genetic and gene expression variations in KYP, CMT3, and IBM1 within and between flowering plant species. IBM1 activity in Arabidopsis thaliana is uniquely regulated by the abundance of H3K9me2 in a repetitive sequence within an intron preceding the histone demethylase domain. This mechanism enables IBM1 to monitor global levels of H3K9me2. We discovered that the methylated intron is prevalent across flowering plants, however, its underlying sequence exhibits dynamic evolution. Its absence in species lacking gene body DNA methylation suggests its primary role in sensing H3K9me2 and preventing its integration into these constitutively expressed genes. Furthermore, our investigation uncovered Arabidopsis thaliana accessions resembling weak ibm1 mutants, several Brassicaceae species with reduced IBM1 expression, and a potential IBM1 deletion. Evolution towards reduced IBM1 activity in some flowering plants could explain the frequent natural occurrence of diminished or lost CMT3 activity, as cmt3 mutants in A. thaliana mitigate the deleterious effects of IBM1.
2024-05-10 | GSE252913 | GEO
Project description:We generated and sequenced ChIP libraries for the meiotic cohesin subunit REC8 and four histone modifications (H3K4me1, H3K4me2, H3K9me2 and H3K27me1) to investigate their relationships with meiotic chromosome architecture and recombination in Arabidopsis thaliana. REC8 and H3K9me2 ChIP-seq were performed using meiotic-stage floral buds from wild type (Col-0) and non-CG DNA methylation/H3K9me2 pathway mutant (kyp/suvh4 suvh5 suvh6 or cmt3) plants to examine the role of heterochromatin assembly in meiotic cohesin distribution.
2020-01-21 | E-MTAB-7370 | biostudies-arrayexpress
Project description:Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution genome-wide maps of both H3K9m2 and H3K27m3 in wild type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that most of the ectopic H3K9m2 observed in met1 is not due to defects in IBM1-mediated H3K9m2 demethylation, but instead targets H3K27m3-marked genes suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whearas H3K9m2 hypomethylated transposons become ectopically H3K27me3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation, but ectopic hypermethylation of genes previously marked by H3K27m3. Keywords: Genome binding/occupancy profiling by genome tiling array We used the met1-3 allele (Saze et al. 2003) and the salk_006042 line for isolating ibm1 mutants. met1-1st generation homozygous mutants and ibm1-1st generation homozygous mutants were isolated from a segragating population by genotyping. met1-2nd generation second mutants are the progeny of a single met1-1st generation homozygous mutant that was partially fertile. The entire shoots of 3 weeks old Arabidopsis plants (Col-0 ecotype), grown for 3 weeks under continuous light, were harvested, cross-linked as described in (Bernatavichute et al., 2007), frozen under liquid nitrogen and grown to powder (2g). Arabidopsis chromatin enriched for H3K9m2 and H3K27m3 was immunoprecipitated using an antibody that specifically recognizes H3K9m2 (Abcam 1220) and an antibody that specifically recognizes H3K27m3 (Upstate 07-449) respectively. Unmodified H3 was immunoprecipitated using Abcam 1791-100. Nucleosomal DNA and Input DNA were used as controls. ChIP, DNA purification and amplification were performed as in (Bernatavichute et al., 2007); Roche Nimblegen performed labelling and hybridization of the samples, washing and scanning resolution. All ChIP signals were normalized with either H3 ChIP or input genomic DNA by taking the log2 ratio and adjusted so that the average log2 ratio score across the genome was zero. 6 samples Processed data can be downloaded at http://danio.pellegrini.mcdb.ucla.edu/~hume/Deleris_PLoSGen2012_H3K9m2data.zip
2016-06-22 | E-GEOD-83606 | biostudies-arrayexpress
Project description:Investigation of genome-wide expression in the mutant of histone H3K9 methyltransferase KRYPTONITE (KYP) or DNA methyltransferase CHROMOMETHYLASE3 (CMT3) in Arabidopsis. These mutants showed decrease in H3K9 methylation and DNA methylation levels, and transcriptional activation at transposons and repeats. Using NimbleGen DNA microarray, global pattern of expression of genes and transposons were examined in these mutants. Total RNA from leaves was isolated using the RNeasy Plant Mini kit (Qiagen) and was treated with DNase I (TAKARA). Double-stranded cDNA was synthesized using the SuperScript Double Stranded cDNA Synthesis kit (Invitrogen) and oligo (dT)20 primer. cDNA was labeled by Cy3, hybridized to 4 x 72k array, and scanned according to manufacture's instructions (www.nimblegen.com).
2010-09-21 | E-GEOD-22957 | biostudies-arrayexpress
Project description:Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution genome-wide maps of both H3K9m2 and H3K27m3 in wild type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that most of the ectopic H3K9m2 observed in met1 is not due to defects in IBM1-mediated H3K9m2 demethylation, but instead targets H3K27m3-marked genes suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whearas H3K9m2 hypomethylated transposons become ectopically H3K27me3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation, but ectopic hypermethylation of genes previously marked by H3K27m3. We used the met1-3 allele (Saze et al. 2003) and the salk_006042 line for isolating ibm1 mutants. met1-1st generation homozygous mutants and ibm1-1st generation homozygous mutants were isolated from a segragating population by genotyping. met1-2nd generation second mutants are the progeny of a single met1-1st generation homozygous mutant that was partially fertile. The entire shoots of 3 weeks old Arabidopsis plants (Col-0 ecotype), grown for 3 weeks under continuous light, were harvested, cross-linked as described in (Bernatavichute et al., 2007), frozen under liquid nitrogen and grown to powder (2g). Arabidopsis chromatin enriched for H3K9m2 and H3K27m3 was immunoprecipitated using an antibody that specifically recognizes H3K9m2 (Abcam 1220) and an antibody that specifically recognizes H3K27m3 (Upstate 07-449) respectively. Unmodified H3 was immunoprecipitated using Abcam 1791-100. Nucleosomal DNA and Input DNA were used as controls. ChIP, DNA purification and amplification were performed as in (Bernatavichute et al., 2007); Roche Nimblegen performed labelling and hybridization of the samples, washing and scanning resolution. All ChIP signals were normalized with either H3 ChIP or input genomic DNA by taking the log2 ratio and adjusted so that the average log2 ratio score across the genome was zero. 6 samples
2013-03-02 | E-GEOD-37075 | biostudies-arrayexpress
Project description:In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the epsilon-ammonium of K9 positioned adjacent to bound SAH. These structural insights complemented by in vivo functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.
2014-08-01 | GSE57963 | GEO
Project description:Methylation of histone H3 lysine 9 (H3K9me) and small RNA 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. The transposon-specific non-CpG methylation in plants is controlled by small RNA and H3K9me. Although it is often assumed that small RNA directs H3K9me, interaction between small RNA and H3K9me has not been directly shown in plants. We have previously shown that a mutation in a chromatin remodeling gene DDM1 (decrease in DNA methylation) induces a global decrease as well as local increase of cytosine methylation and accumulation of small RNA in a locus called BONSAI. Here we show that the de novo BONSAI methylation does not depend on RNAi but depends on H3K9me. Notably, in mutant of H3K9 methylase gene KRYPTONITE or H3K9me-dependent DNA methylase 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 ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications, which could be conserved among diverse eukaryotes. comparison of DNA methylation between WT, 2G ddm1 (2 replications), 8G ddm1 (2 replications), and 8G ddm1 kyp
2011-12-25 | E-GEOD-34222 | biostudies-arrayexpress
Project description:DNA methylation occurs at preferred sites in eukaryotes, although the basis for preference is not known. We use a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related RNA silencing component (AGO4) in methylating target loci. We find that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that corresponds to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants. Our results suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism. Thus, parallel pathways would be needed to maintain silencing of transposable elements. Keywords: Methylation profiling using Msp I enzyme
2005-10-25 | GSE3109 | GEO