Maize DDM1 targets RNA-directed DNA methylation on active chromatin
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE162678 | GEO | 2020/12/05
REPOSITORIES: GEO
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Project description:Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. We also show that small RNA-directed DNA methylation (RdDM) is inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. DDM1 and RdDM independently mediate nearly all transposon methylation, which is catalyzed by the methyltransferases MET1 (CG), CMT3 (CHG), DRM2 (CHH) and CMT2 (CHH), and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that the Arabidopsis genome is defined by a heterochromatic continuum that governs the access of DNA methyltransferases and potentially all DNA binding proteins. Examination of DNA methylation, transcription and nucleosomes in Arabidopsis wild-type and/or ddm1, RdDM and DNA methylase mutants.
2013-04-17 | E-GEOD-41302 | biostudies-arrayexpress
Project description:Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. We also show that small RNA-directed DNA methylation (RdDM) is inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. DDM1 and RdDM independently mediate nearly all transposon methylation, which is catalyzed by the methyltransferases MET1 (CG), CMT3 (CHG), DRM2 (CHH) and CMT2 (CHH), and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that the Arabidopsis genome is defined by a heterochromatic continuum that governs the access of DNA methyltransferases and potentially all DNA binding proteins.
2013-04-17 | GSE41302 | GEO
Project description:DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.
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Project description:DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.
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Project description:DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.
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Project description:DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. We establish that ZmDDM1 is critical for DNA methylation, at CHG sites, and to a lesser extent at CG sites, in heterochromatic regions, and unexpectedly, it is required for the formation of m CHH islands. In addition, ZmDDM1 is indispensable for the presence of 24-nt siRNA, suggesting its involvement in the RdDM pathway. Our results provide novel insight into the role of ZmDDM1 in regulating the formation of m CHH islands, via the RdDM pathway maize, suggesting that, in comparison to Arabidopsis, maize may have adopted distinct mechanisms for regulating m CHH.
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Project description:In this work, we studied function of rice DDM1 in coordinating DNA methylation, expression of small (sRNA) and long noncoding (lncRNA) RNAs, and nucleosome positioning by high throughput approaches.We show that the ddm1a/1b mutation resulted in ectopic CHH methylation of transposable elements (TE) and repeats. The ectopicCHH methylationwas dependent on DRM2, a DNA methyltransferase involved in sRNA-dependent DNA-methylation (RdDM). The ddm1a/1b mutation resulted in increases of heterochromatic sRNA but decreases of euchromatic sRNA production,induced expression of a set of developmentally regulated heterochromatic lncRNA , and increased nucleosome occupancy of TE-related or silent genes including heterochromatic lncRNA loci. In particular,DDM1-mediated repression ofCentromericRetrotransposons of Rice1 (CRR1) was essential for centromere function.
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Project description:Nodulin homeobox (NDX) is a nuclear protein described as the regulator of specific euchromatic genes that controls multiple aspects of Arabidopsis development. At the molecular level, NDX was shown to i) interact with the Polycomb repressive complex 1 (PRC1) to promote deposition of repressive histone marks at abscisic acid-responsive gene loci, and (ii) stabilize an R-loop structure within the Flowering Locus C (FLC) to control its expression. Herein, we aimed to understand the global role of NDX in chromatin-based gene regulation and comprehensively characterized its genomic binding sites and transcriptional relationships involving sRNA profiling, DNA methylation, and 3D chromatin structure. Using quantitative microscopic and genomics approaches we show that NDX is a highly immobile heterochromatic protein that localizes primarily to centromeres and pericentromeric regions. Most NDX binding sites coincide with heterochromatic sRNA loci that are known to mediate transcriptional gene silencing via the RNA-dependent DNA methylation (RdDM) pathway. NDX localization was antagonistic with R-loop structures that were prevalent in euchromatic chromosomal arms. Functional analysis revealed that the absence of NDX led to differential hypo- and hyper-methylation in the CG / CHG / CHH sequence context, of which hypo-CHH / CHG sites were co-localized with NDX chromatin binding sites. The identified hypo-CHH/CHGs were associated with increased heterochromatic sRNA production (predominantly 24nt sRNAs) and parallel transcriptional activation of pericentric transposons. Chromosome conformation capture (Hi-C) revealed significant chromatin structural changes in the ndx mutant, with decreased intra-chromosomal interactions (chromatin decompaction) at pericentromeric regions where NDX is enriched in wild type plants, and increased inter-chromosomal contacts between KNOT-forming regions. KNOT interactions involved de novo interchromosomal contacts similar to genome structural changes observed in DNA methylation mutants. We conclude that the main role of NDX is the functional regulation of heterochromatin, which is mechanistically coupled to the effector phase of the RdDM pathway.
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Project description:Nodulin homeobox (NDX) is a nuclear protein described as the regulator of specific euchromatic genes that controls multiple aspects of Arabidopsis development. At the molecular level, NDX was shown to i) interact with the Polycomb repressive complex 1 (PRC1) to promote deposition of repressive histone marks at abscisic acid-responsive gene loci, and (ii) stabilize an R-loop structure within the Flowering Locus C (FLC) to control its expression. Herein, we aimed to understand the global role of NDX in chromatin-based gene regulation and comprehensively characterized its genomic binding sites and transcriptional relationships involving sRNA profiling, DNA methylation, and 3D chromatin structure. Using quantitative microscopic and genomics approaches we show that NDX is a highly immobile heterochromatic protein that localizes primarily to centromeres and pericentromeric regions. Most NDX binding sites coincide with heterochromatic sRNA loci that are known to mediate transcriptional gene silencing via the RNA-dependent DNA methylation (RdDM) pathway. NDX localization was antagonistic with R-loop structures that were prevalent in euchromatic chromosomal arms. Functional analysis revealed that the absence of NDX led to differential hypo- and hyper-methylation in the CG / CHG / CHH sequence context, of which hypo-CHH / CHG sites were co-localized with NDX chromatin binding sites. The identified hypo-CHH/CHGs were associated with increased heterochromatic sRNA production (predominantly 24nt sRNAs) and parallel transcriptional activation of pericentric transposons. Chromosome conformation capture (Hi-C) revealed significant chromatin structural changes in the ndx mutant, with decreased intra-chromosomal interactions (chromatin decompaction) at pericentromeric regions where NDX is enriched in wild type plants, and increased inter-chromosomal contacts between KNOT-forming regions. KNOT interactions involved de novo interchromosomal contacts similar to genome structural changes observed in DNA methylation mutants. We conclude that the main role of NDX is the functional regulation of heterochromatin, which is mechanistically coupled to the effector phase of the RdDM pathway.
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Project description:Nodulin homeobox (NDX) is a nuclear protein described as the regulator of specific euchromatic genes that controls multiple aspects of Arabidopsis development. At the molecular level, NDX was shown to i) interact with the Polycomb repressive complex 1 (PRC1) to promote deposition of repressive histone marks at abscisic acid-responsive gene loci, and (ii) stabilize an R-loop structure within the Flowering Locus C (FLC) to control its expression. Herein, we aimed to understand the global role of NDX in chromatin-based gene regulation and comprehensively characterized its genomic binding sites and transcriptional relationships involving sRNA profiling, DNA methylation, and 3D chromatin structure. Using quantitative microscopic and genomics approaches we show that NDX is a highly immobile heterochromatic protein that localizes primarily to centromeres and pericentromeric regions. Most NDX binding sites coincide with heterochromatic sRNA loci that are known to mediate transcriptional gene silencing via the RNA-dependent DNA methylation (RdDM) pathway. NDX localization was antagonistic with R-loop structures that were prevalent in euchromatic chromosomal arms. Functional analysis revealed that the absence of NDX led to differential hypo- and hyper-methylation in the CG / CHG / CHH sequence context, of which hypo-CHH / CHG sites were co-localized with NDX chromatin binding sites. The identified hypo-CHH/CHGs were associated with increased heterochromatic sRNA production (predominantly 24nt sRNAs) and parallel transcriptional activation of pericentric transposons. Chromosome conformation capture (Hi-C) revealed significant chromatin structural changes in the ndx mutant, with decreased intra-chromosomal interactions (chromatin decompaction) at pericentromeric regions where NDX is enriched in wild type plants, and increased inter-chromosomal contacts between KNOT-forming regions. KNOT interactions involved de novo interchromosomal contacts similar to genome structural changes observed in DNA methylation mutants. We conclude that the main role of NDX is the functional regulation of heterochromatin, which is mechanistically coupled to the effector phase of the RdDM pathway.
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