Oryza sativa
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-39298
PROVIDER: PRJNA175323 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2) are important epigenetic repression marks for silencing transposons in heterochromatin and regulating gene expression in plant development. However, the mechanistic relationship to other repressive marks, such as histone H3 lysine 27 trimethylation (H3K27me3), is unclear. OsFIE1 (Fertilization Independent Endosperm 1) encodes an Esc-like core component of the Polycomb repressive complex 2 (PRC2), which is involved in H3K27me3-mediated gene repression. Here, we identify a gain-of-function epi-allele (Epi-df) of rice OsFIE1; this allele exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We found that Epi-df has no changes in its nucleotide sequence, but is hypo-methylated in the promoter and the 5' region of OsFIE1 and has reduced H3K9me2 and increased H3K4me3. In Epi-df, OsFIE1 was ectopically expressed and its imprinting status was disrupted. OsFIE1 interacted with rice E(z) homologs, consistent with its role in H3K27me3 repression. Ectopic expression of OsFIE1 in Epi-df resulted in alteration of H3K27me3 levels in hundreds of genes. Therefore, this work identifies a novel epi-allele involved in H3K27me3-mediated gene repression, that itself is highly regulated by histone H3K9me2, thereby shedding light on the link between two important epigenetic marks regulating rice development. We report the application of ChIP-Seq technology for high-throughput profiling of histone modifications in WT (wild type) and Epi-df (mutant). We demonstrate that the H3K27me3 status is perturbed at target genes and leads to mis-regulated expression in Epi-df.
2013-12-04 | E-GEOD-40674 | biostudies-arrayexpress
Project description:We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes. We used microarrays to identify differentially expressed genes in Epi-df. For genome-wide expression analysis of Epi-df, three replicates of WT and Epi-df samples (RNA from 3-week-old seedlings) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.
2012-07-12 | E-GEOD-39298 | biostudies-arrayexpress
Project description:We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes. We used microarrays to identify differentially expressed genes in Epi-df.
2012-07-13 | GSE39298 | GEO
Project description:DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2) are important epigenetic repression marks for silencing transposons in heterochromatin and regulating gene expression in plant development. However, the mechanistic relationship to other repressive marks, such as histone H3 lysine 27 trimethylation (H3K27me3), is unclear. OsFIE1 (Fertilization Independent Endosperm 1) encodes an Esc-like core component of the Polycomb repressive complex 2 (PRC2), which is involved in H3K27me3-mediated gene repression. Here, we identify a gain-of-function epi-allele (Epi-df) of rice OsFIE1; this allele exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We found that Epi-df has no changes in its nucleotide sequence, but is hypo-methylated in the promoter and the 5' region of OsFIE1 and has reduced H3K9me2 and increased H3K4me3. In Epi-df, OsFIE1 was ectopically expressed and its imprinting status was disrupted. OsFIE1 interacted with rice E(z) homologs, consistent with its role in H3K27me3 repression. Ectopic expression of OsFIE1 in Epi-df resulted in alteration of H3K27me3 levels in hundreds of genes. Therefore, this work identifies a novel epi-allele involved in H3K27me3-mediated gene repression, that itself is highly regulated by histone H3K9me2, thereby shedding light on the link between two important epigenetic marks regulating rice development.
2013-12-04 | GSE40674 | GEO
Project description:Comparison of transcriptome profile between wild-type and Epi-df mutant plants
| PRJNA170511 | ENA
Project description:By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice. The transcriptional profiling between the wild-type rice and an Al-sensitive mutant, star1. +Al vs. -Al in the roots of wild-type rice and star1 mutant. Biological replicates: +Al/-Al WT root tip 4 replicates, +Al/-Al WT basal tip 4 replicates, +Al/-Al star1 root tip 4 replicates, +Al/-Al star1 basal tip 4 replicates
2012-09-19 | E-GEOD-40964 | biostudies-arrayexpress
Project description:In our study, we identified a new transgenerational epigenetic mutant in rice, Epi-LF (Epi-LongFeng). The metastable phenotype of Epi-lf resembles that of rice Epi-d1, and the inheritance is largely similar to that of the agoutiAy mouse mutant. We found that in Epi-lf,mCHH methylation was present in a 155-bp sequence of DNA in close proximity to the 3' end of the LF gene, but the abundance of the siRNAs corresponding to this region was not significantly different from that of the wild type (WT), suggesting that this is a mCHH island like modification. In addition, ectopic mCHH modifications accumulated in the sporophytic tissues and embryos of the Epi-lf mutants. The majority of these ectopic CHH regions did not fit with the OsDRM2 (Domain Rearranged Methylase2)-mediated CHH methylation of genomic regions, suggesting that unknown genetic factors may co-ordinate DNA demethylation and methylation, especially for non-CG methylation.
2021-07-01 | GSE133741 | GEO
Project description:To reveal the underlying molecular mechanism of jasmonate inhibits gibberellins signaling in rice, we performed transcriptional profiling of wild type nipponbare and mutant coi1-13 plants on a global scale using the Affymetrix GeneChip Rice Genome Array
2011-12-01 | GSE29577 | GEO
Project description:By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice.
2012-09-19 | GSE40964 | GEO
Project description:To reveal the underlying molecular mechanism of jasmonate inhibits gibberellins signaling in rice, we performed transcriptional profiling of wild type nipponbare and mutant coi1-13 plants on a global scale using the Affymetrix GeneChip Rice Genome Array Rice young uppermost internodes were harvested and three biological repeats were performed on Nippombare (wild-type) and coi1-13 (mutant), respectively.
2011-12-01 | E-GEOD-29577 | biostudies-arrayexpress