WGBS of Arabidopsis thaliana COM-edm2 mutant
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ABSTRACT:
PROVIDER: PRJNA956973 | ENA |
REPOSITORIES: ENA
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Project description:Here we address that a mutation of EDM2 (Enhanced Downy Mildew 2), which is regarded as regulator of genome DNA methylation patterns, displays abnormal cotyledon number and shorted root length. Further, in early embryogenesis, edm2 shows embryonic developmental abnormalities, including the appearance of asymmetric embryos at the heart stage and unclear boundary between the spherical proembryo and suspensor cells. In addition, dysfunction of EDM2 alters the level of the auxin transporter PINs (PIN-FORMEDs), consistent with disordered distribution of auxin, which maybe the reason for developmental defect. Interestingly, analysis of high-throughput sequencing data show that the loss-of-function EDM2 exhibits the decreased expression of auxin polar transport-related gene PLT1 (PLETHORA 1), while methylation level and H3K9me2 enrichment in gene body are slightly higher than that in wide type. These results advance our understanding of EDM2 in establishment of auxin gradients through epigenetic modification and elucidate the roles of EDM2 in early embryogenesis.
2023-04-23 | GSE230021 | GEO
Project description:WGBS of Arabidopsis thaliana rll6 mutant
| PRJNA859377 | ENA
Project description:EDM2 is a PHD finger-containing histone binding protein in Arabidopsis thaliana (Arabidopsis) that affects levels of the transposon silencing mark H3K9me2. Here we report on genome-wide profiling by ChIP-seq and RNA-seq of EDM2-mediated effects on H3K9me2 and rRNA-depleted transcripts, respectively. EDM2 affects H3K9me2 and/or transcript levels at hundreds transposons and over 3000 gene loci including 60 NLR genes. In addition, EDM2 also binds to several NLR genes and transposons.
2020-08-03 | GSE108487 | GEO
Project description:Seedlings of Arabidopsis thaliana Col-0 were treated with a cutin oligomeric mixture (COM) for 30 min. To evaluate if such treatment was able to induce transcriptional reprogramming related with plant immunity. The transcriptomic profiles were compared with those of the Mock treatment. The list of differentially expressed genes was generated to evaluate similarities with the profiles obtained with treatments with well described plant immune elicitors.
2023-10-31 | E-MTAB-12956 | biostudies-arrayexpress
Project description:We perform genome-wide profiling of H3K9me2 in the Arabidopsis thaliana edm3 mutant. By var-seq, we identified EDM3 as a nuclear-localized protein featuring a single RNA-recognition motif (RRM). Similar to PHD finger-containing histone binding protein EDM2, EDM3 promotes high levels of H3K9me2 at RPP7 and controls transcripts of this NLR gene by suppressing proximal polyadenylation and promoting the synthesis of full-length RPP7-coding mRNAs. Our results showed that EDM3 affects levels of this epigenetic mark at a set of genes and transposons, the vast majority of which also feature EDM2-dependent H3K9me2.
2020-01-29 | GSE108490 | GEO
Project description:Transcriptome of Arabidopsis thaliana mem1-1 mutant and Col-0 under normal and 200ppm MMS treatment conditions, respectively
2021-08-04 | GSE181302 | GEO
Project description:Comparative study of nuclesome occupancy in Arabidopsis thaliana mutant chr5 and wild type strain.
2019-05-23 | GSE99639 | GEO
Project description:Arabidopsis thaliana mutant sr45-1 has an altered flower shape. sr45 is a splicing regulator. In this study, we examined the proteins from inflorescence of sr45-1 mutant plants and wild-type. Wild type TMT labels: 126, 128, 130. sr45-1 TMT labels: 127, 129, 131.
2019-04-26 | MSV000083728 | MassIVE
Project description:The Arabidopsis thaliana defense regulator EDM2 was previously shown to be specifically required for disease resistance to the pathogenic oomycete Hyaloperonospora parasitica aradidopsis mediated by the R protein RPP7. We found EDM2 to have a promoting effect on several distinct developmental processes, such as leaf pavement cell development, vegetative phase change or the floral transition. We further identified the atypical protein kinase WNK8 to physically interact with EDM2 in nuclei. Microarray data support regulatory interactions between WNK8 and EDM2 as well as their functional association with the autonomous floral promotion pathway.
2010-09-21 | GSE17499 | GEO
Project description:To gain deeper insights into the mechanisms of DNA demethylation pathway, we conducted a genetic screen for proteins that are involved in preventing epigenetic silencing, and then the ones, which are also implicated in DNA demethylation pathway, are used for further studies. Eventually, a mutant with low luciferase luminescence (low LUC luminescence) was recovered, and named reduced LUC luminescence 6-1 (rll6-1). Map-based cloning revealed thatrll6-1 mutation is located in bacterial artificial chromosome (BAC) clone F5I10 on chromosome 4, and there are a total of 10 candidate genes were found within such a region. Analysis of genome-wide methylation patterns of rll6-1 mutant showed that rll6-1 mutation led to 3863 hyper-DMRs throughout the five Arabidopsis chromosomes, and elevated DNA methylation level of 2×35S promoter, which was similar to that found in ros1 mutant. Further analysis demonstrated that there are 1456 common hyper-DMRs shared by rll6-1 and ros1-7, which account for 2407 and 5642 hyper-DMRs, respectively, suggesting both proteins act together in a synergistic manner to remove DNA methylation. Further investigations demonstrated that rll6-1 mutation does not affect the expression of the four genes of the DNA glycosylase/lyase family. Thus, our results demonstrated that RLL6 not only participated in transcriptional anti-silencing, but is also involved in DNA demethylation pathway.
2022-07-17 | GSE208332 | GEO