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.
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.
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.
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.
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.
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.
Project description:CAF-1 is a major nucleosome assembly complex, which functions particularly during replication and DNA-repair. Here, we studied how the nucleosome landscape changes in fas2 a mutant of the CAF-1 complex in the model plant Arabidopsis thaliana