Tomato ddm1 mutants
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ABSTRACT:
PROVIDER: PRJEB23761 | ENA |
REPOSITORIES: ENA
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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:DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. In contrast to recent discoveries that DNA demethylation is critical for tomato fruit ripening, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR-Cas9 gene editing, we generated slmet1 mutants and discovered that SlMET1 is required for normal development of flowers and seeds in tomato. Mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole-genome scale, leading to a disturbed transcriptome including defects in the expression of key genes involved in meristem formation, seed development and fruit ripening. Consistently, the slmet1 mutants showed impaired flower production, elevated lycopene levels in fruits, and pathenocarpic fruits. In the slmet1 mutants, hypomethylated CG and hypermethylated CHH cytosines are preferentially located in genes and transposable elements (TEs), respectively. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture-induced non-CG hypomethylation, which prefers genes over TEs and is more stable in the former regions than the latter during subsequent inbreeding. Our results depict SlMET1- and tissue culture-dependent tomato DNA methylomes, and that SlMET1 is required for normal development of flowers and seeds, thereby highlighting a role of DNA methylation in determining the yield of normal tomato fruits.
2019-01-22 | GSE102273 | GEO
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.
2018-06-06 | GSE108527 | GEO
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: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:Transcriptome data from tomato parthenocarpic mutants
| PRJNA742258 | ENA
Project description:We investigated the behavior of tomato mutants lacking transcription factors of TAP3, a class B MADS-box gene controlling parthenocarpy. To focus on the early stages of anthesis, ovary samples of MicroTom-J (MT-J) and the mutant at the different stages (e.g., bud, flowering, and after flowering) were collected.
2022-05-18 | GSE179026 | GEO
Project description:Transcriptome data from tomato parthenocarpic mutants lacking Tomato APETALA3 (TAP3)
| PRJNA741939 | ENA
Project description:We investigated the behavior of tomato mutants lacking SlDELLA, a negative regulator of gibberellin (GA) signaling pathway. To focus on the early stages of anthesis, ovary samples of MicroTom-B (MT-B) and the mutant at the three stages (bud, flowering, and after flowering) were collected.
2022-05-18 | GSE179025 | GEO
Project description:Background: Transposable elements are known to influence the regulation of some genes. We aimed to determine which genes show altered gene expression when transposable elements are epigenetically activated. Results: We find over 2000 genes with altered steady-state expression levels in ddm1 mutants. Some of these genes are influenced by neighboring transposable element fragments, while other genes are targeted by transposable element derived 21 nucleotide siRNAs. Conclusion: The regulation of the genic portion of the Arabidopsis genome is heavily influenced by the epigenetic regulation of transposable elements. The regulation of genes by transposable elements can occur through multiple mechanisms.
2014-04-07 | GSE46050 | GEO