Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA149817 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To generate epi-lines, two third-generation msh1 T-DNA mutant (SAIL_877_F01) plants were used to pollinate Col-0 to generate two independent F1 populations. Derived F1 progenies were self-pollinated to generate F2 populations that were genotyped for the msh1 T-DNA mutation. MSH1 F2 plants were self-pollinated to produce F3 families that were used in the study.
2022-07-08 | GSE192429 | GEO
Project description:To generate epi-lines, two third-generation msh1 T-DNA mutant (SAIL_877_F01) plants were used to pollinate Col-0 to generate two independent F1 populations. Derived F1 progenies were self-pollinated to generate F2 populations that were genotyped for the msh1 T-DNA mutation. MSH1 F2 plants were self-pollinated to produce F3 families that were used in the study.
2022-07-08 | GSE192428 | 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:Here we present the proteomic profile of mutant plants designated as eds16 (enhanced disease susceptibility), ceh1 (constitutively expressing HPL) as well as the ceh1 eds16 double mutant. CEH1 encodes 1-hydroxy-2-methyl-2-butenyl 4-diphosphate synthase (HDS), the enzyme controlling the bottleneck step of the biosynthesis of isopentenyl diphosphate via the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway in the plastids. Mutation of this enzyme in ceh1 mutant led to accumulation of high levels of the stress specific signaling metabolite 2c-methyl-D-erythritol 2,4-cylclodiphosphate (MEcPP), and consequently constitutive activation of a selected otherwise stress responsive genes. This data identifies the ensemble of stress responsive genes whose expression is regulated by the MEcPP signaling cascade.
| MSV000078868 | MassIVE
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:The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. However, the global targets of the non-canonical RdDM pathway are unidentified. In an attempt to identify and contrast the targets of canonical and non-canonical RdDM, we sequenced small RNAs from several RdDM mutants in either the TE-silent or the TE-active (ddm1) contexts. Examination of unopened flower bud small RNAs from wild type and various single or double mutant combinations, many of which have biological replicates. Small RNA sequences from wt Col, controls and other mutants shown in the study are available at GSE41755 and GSE57191.
2016-07-22 | E-GEOD-79780 | 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. Plants homozygous for null mutations in the KRYPTONITE H3K9 methyltransferase were stably transformed with transgenes encoding the wildtype KYP protein or transgenes carrying induced point mutations in the KYP active site. The resulting lines were assayed for DNA methylation by whole-genome bisulfite sequencing to learn the efficiency with which wildtype and mutant versions of the KYP protein could restore DNA methylation lost in a kyp mutant. Samples 7 and 8 were run as single Illumina lanes and as such were compared to a previous Col sample (GSM881756), this Col sample was realigned to the TAIR10 genome for this study and as such updated processed files are available with this submission. These samples were used to define kyp mutant CHG context DMRs that were complemented upon introduction of the wildtype KYP protein. Samples 1-6 were run as multiplexed samples and were used to assay the degree of complementation for various point mutants. All plants are in the Col ecotype background.
2014-08-01 | E-GEOD-57963 | 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.
2010-09-21 | GSE22957 | GEO
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of KYP in 10 days old KYPpro::KYP:3xFLAG arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide binding levels of KYP:3xFLAG. ChIP was performed using anti-FLAG antibody (sigma M2), and ChIP DNA were analyzed by Illumina NovoSeq.
2023-03-01 | GSE195735 | GEO
Project description:To generate msh1 memory revertant population, msh1 memory plant was used to pollinate Col-0 to generate F1 population. Derived F1 progenies were self-pollinated to generate F2 populations. F2 plants were self-pollinated to produce F3 families that were segregationg for the msh1 memory phenotype (small dwarf plants with delayed flowering).
2022-07-08 | GSE192432 | GEO