Ontology highlight
ABSTRACT:
PROVIDER: PRJNA575572 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10228069_1.fastq.gz | Fastqsanger.gz | |||
| SRR10228069_2.fastq.gz | Fastqsanger.gz | |||
| SRR10228070_1.fastq.gz | Fastqsanger.gz | |||
| SRR10228070_2.fastq.gz | Fastqsanger.gz | |||
| SRR10228071_1.fastq.gz | Fastqsanger.gz |
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Project description:Experimental DNA demethylation associates with changes in phenotype and gene expression of tree seedlings
| PRJNA574633 | ENA
Project description:Epigenetic modifications, such as DNA methylation where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence the ability of plants to respond to changing environmental conditions. One approach to determining the association between DNA methylation, phenotypic variation, and gene expression, is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree species of Quercus lobata with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that foliar application of 5-azayctidine lead to a 3-6% absolute reduction and 6.1-43% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. We also show that the demethylation treatment had minimal impact on the soil microbiome. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings, and but no significant differences in fluctuating asymmetry (i.e., deviations from bilateral symmetry) of leaves compared to control seedlings. Finally, treated seedlings showed differential expression of a total of 23 genes relative to control seedlings, the majority of which were upregulated. Overall, this study provides evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings.
2019-09-28 | GSE138108 | GEO
Project description:Active DNA demethylation is an important epigenetic phenomenon in many eukaryotes. In Arabidopsis thaliana, ROS1, a 5-methylcytosine DNA glycosylase, is responsible for active DNA demethylation via a base excision repair process. Here, we found that Bromodomain and ATPase domain-containing protein 1 (BRAT1) associates with BRP1 (BRAT1 Partner 1) and forms a tight BRAT1–BRP1 complex required for DNA demethylation. To identify hypermethylated loci at the whole-genome level in brat1, brp1, and ros1, we performed whole-genome bisulfite sequencing. Compare the DNA methylation profiles of 10-day old seedlings materials of mutants (brat1, brp1, and ros1) to wild type by whole-genome bisulfite sequencing.
2015-04-14 | E-GEOD-67798 | biostudies-arrayexpress
Project description:Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. So far, it was unclear how mammals specifically achieve global DNA hypomethylation, given the high conservation of the DNA (de-)methylation machinery among vertebrates. We found that DNA demethylation requires TET activity but mostly occurs at sites where TET proteins are not bound suggesting a rather indirect mechanism. Among the few specific genes bound and activated by TET proteins was the naïve pluripotency and germline marker Dppa3 (Pgc7, Stella), which undergoes TDG dependent demethylation. The requirement of TET proteins for genome-wide DNA demethylation could be bypassed by ectopic expression of Dppa3. We show that DPPA3 binds and displaces UHRF1 from chromatin and thereby prevents the recruitment and activation of the maintenance DNA methyltransferase DNMT1. We demonstrate that DPPA3 alone can drive global DNA demethylation when transferred to amphibians (Xenopus) and fish (medaka), both species that naturally do not have a Dppa3 gene and exhibit no post-fertilization DNA demethylation. Our results show that TET proteins are responsible for active and - indirectly also for - passive DNA demethylation; while TET proteins initiate local and gene-specific demethylation in vertebrates, the recent emergence of DPPA3 introduced a unique means of genome-wide passive demethylation in mammals and contributed to the evolution of epigenetic regulation during early mammalian development.
2020-10-12 | PXD019794 | Pride
Project description:Active DNA demethylation is an important epigenetic phenomenon in many eukaryotes. In Arabidopsis thaliana, ROS1, a 5-methylcytosine DNA glycosylase, is responsible for active DNA demethylation via a base excision repair process. Here, we found that Bromodomain and ATPase domain-containing protein 1 (BRAT1) associates with BRP1 (BRAT1 Partner 1) and forms a tight BRAT1–BRP1 complex required for DNA demethylation. To identify hypermethylated loci at the whole-genome level in brat1, brp1, and ros1, we performed whole-genome bisulfite sequencing.
2015-04-14 | GSE67798 | GEO
Project description:We investigated the effects of experimental EBV infection of B cells on DNA methylation profiles by using high-throughput analysis. Remarkably, we observed hypomethylation of around 250 genes, but no hypermethylation. Hypomethylation did not occur at repetitive sequences, consistent with the absence of genomic instability in lymphoproliferative cells. Changes in methylation only occurred after cell divisions started, without the participation of the active demethylation machinery, and were concomitant with acquisition of B cells of the ability to proliferate. Gene ontology analysis, expression profiling, high-throughput analysis of the presence of transcription factor-binding motifs and occupancy revealed that most genes undergoing hypomethylation are active and display the presence of NFkB p65 and other B cell-specific transcription factors. Promoter hypomethylation associated with upregulation of genes relevant for the phenotype of proliferating lymphoblasts. Interestingly, pharmacologically-induced demethylation increased the efficiency of transformation of resting B cells to lymphoblastoid cells, suggesting the establishment of a productive cooperation between hypomethylation and lymphocyte proliferation. Bisulfite-converted DNA from 12 samples (6 Bcell, 6 Bcell immortalized) were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.
2012-12-20 | E-GEOD-41957 | biostudies-arrayexpress
Project description:Overexpression of programmed cell death 5 gene (PDCD5) in tumor cells enhances apoptosis triggered by growth factor or serum deprivation, and overexpression of its homolog, OsPDCD5, induces the early death of transgenic plants. In this work, a system of inducible OsPDCD5 expression using a heat shock promoter was developed to study PCD in rice at different developmental stages.The results showed that in three-leaf aged and older seedlings, OsPDCD5 could independently induce PCD. In altered plants, OsPDCD5 expression caused lesion mimic phenotype, abnormal leaf morphology, nuclear condensation, DNA fragmentation, and H2O2 production. But two-leaf aged and younger seedlings seedlings showed no visibly morphological phenotype after OsPDCD5 expression, suggested that young seedlings possessed some mechanism inhibiting OsPDCD5 induced PCD.
2011-06-30 | GSE18900 | GEO
Project description:We investigated the effects of experimental EBV infection of B cells on DNA methylation profiles by using high-throughput analysis. Remarkably, we observed hypomethylation of around 250 genes, but no hypermethylation. Hypomethylation did not occur at repetitive sequences, consistent with the absence of genomic instability in lymphoproliferative cells. Changes in methylation only occurred after cell divisions started, without the participation of the active demethylation machinery, and were concomitant with acquisition of B cells of the ability to proliferate. Gene ontology analysis, expression profiling, high-throughput analysis of the presence of transcription factor-binding motifs and occupancy revealed that most genes undergoing hypomethylation are active and display the presence of NFkB p65 and other B cell-specific transcription factors. Promoter hypomethylation associated with upregulation of genes relevant for the phenotype of proliferating lymphoblasts. Interestingly, pharmacologically-induced demethylation increased the efficiency of transformation of resting B cells to lymphoblastoid cells, suggesting the establishment of a productive cooperation between hypomethylation and lymphocyte proliferation.
2012-12-20 | GSE41957 | GEO
Project description:DNA methylation is important for silencing genes and transposable elements. Changes in DNA methylation can be heritable and thus, the loss or gain of methylation can lead to the formation of stable epialleles. A well characterized example of a stable epiallele in plants is fwa-4, which consists of the loss of DNA cytosine methylation (5mC) in the promoter of the FLOWERING WAGENINGEN (FWA) gene, causing upregulation of FWA and a heritable late flowering phenotype. Here we demonstrate that a fusion between the catalytic domain of the Human demethylase TEN-ELEVEN TRANSLOCATION1 (TET1cd) and an artificial zinc finger (ZF) designed to target the FWA promoter can cause highly efficient targeted demethylation, FWA upregulation, and a heritable late flowering phenotype. Additional ZF-TET1cd fusions designed to target methylated regions of the CACTA1 transposon also caused targeted demethylation and changes in expression. Finally, we have developed a CRISPR/dCAS9 based targeted demethylation system using the TET1cd and a modified SunTag system and demonstrate its ability to target demethylation at and activate the expression of FWA and CACTA1. Our study provides tools for targeted removal of 5mC at specific loci in the genome with high specificity and minimal off-target effects. These tools provide the opportunity to develop new epialleles for traits of interest, and to reactivate expression of previously silenced genes, transgenes, or transposons.
2018-02-18 | GSE109115 | GEO
Project description:Interventions: Gold Standard:Clinical outcome;Index test:RAS phenotypic changes in ctDNA
Primary outcome(s): RAS gene phenotype;SEN, SPE, ACC, AUC of ROC
Study Design: Sequential
| 2687923 | ecrin-mdr-crc