Active DNA demethylation controls transgenerational epigenetic stability
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE166343 | GEO | 2024/05/23
REPOSITORIES: GEO
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Project description:Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes. Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of genomic loci. However, the features of ROS1 targets are not well understood. In this study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1 targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants. Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of WT, ros1-4, nrpd1 single mutants and ros1-4/nrpd1doubble mutant
2016-11-01 | GSE83800 | GEO
Project description:Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to wild-type Col-0. The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press).
2014-08-20 | GSE60508 | GEO
Project description:Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to wild-type Col-0. The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press). A twelve chip study using total RNA recovered from three week-old plants grown on Murashige Skoog sucrose agar. The number of biological replicates for each plant genotype were as follows: Col-0 (3 biological replicates), rdd (2), nrpd1 (2) and nrpe1 (2) respectively. Each array contains 60-mer probes targeting 39,042 genes (TAIR 9.0) with 4 probes per gene.
2014-08-20 | E-GEOD-60508 | biostudies-arrayexpress
Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in WT, nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant
2016-11-01 | GSE72280 | GEO
Project description:Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes. Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of genomic loci. However, the features of ROS1 targets are not well understood. In this study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1 targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants.
2016-11-01 | GSE83801 | GEO
Project description:The 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Using a methylation-sensitive PCR (CHOP-PCR)-based forward genetic screen for Arabidopsis DNA hypermethylation mutants, we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation. Dysfunction of SIZ1 leads to hyper-methylation at approximately one thousand genomic regions. SIZ1 physically interacts with ROS1 and mediates the SUMOylation of ROS1. The SUMOylation of ROS1 is reduced in siz1 mutant plants. Compared to that in wild type plants, the protein level of ROS1 is significantly decreased, even though there is an increased level of ROS1 transcripts in siz1 mutant plants. Our results suggest that SIZ1 positively regulates active DNA demethylation by promoting the stability of ROS1 protein through SUMOylation.
2020-06-14 | GSE152425 | GEO
Project description:The transgenerational stability of DNA methylation changes is important in setting up genomic DNA methylation patterns and in the formation and transmission of epialleles. It is generally assumed that DNA methylation changes at genomic regions targeted by the de novo, RNA-directed DNA methylation (RdDM) pathway are unstable. Here, we show that RdDM targets in Arabidopsis can be classified into two groups based on their transgenerational epiallele stability following restoration of NRPD1 function in nrpd1 mutant plants: remethylable loci and non-remethylable loci. Compared to the remethylable loci, non-remethylable ones contain higher levels of the euchromatic marks H3K4me3 and H3K18ac, which interferes with the recruitment of the RdDM molecular machinery and helps to recruit the DNA demethylase ROS1 to antagonize RdDM, respectively. Using targeted de-methylation by CRISPR/dCas9-TET1, we demonstrate that mCG and mCHG are memory marks required for targeting the RdDM machinery to remethylable loci. Our results show that histone and DNA methylation marks are critical in determining the capacity of RdDM target loci to form stable epialleles, and contribute to understanding the formation and transmission of epialleles.
2020-04-17 | GSE140566 | GEO
Project description:Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).
2022-11-07 | GSE211295 | GEO
Project description:Maintenance of CG methylation (mCG) patterns is essential for chromatin-mediated epigenetic regulation of transcription in plants and mammals. Using successive generations of an Arabidopsis thaliana mutant deficient in maintaining mCG, we found that mCG loss triggered genome-wide activation of alternative epigenetic mechanisms. However, these mechanisms involving RNA-directed DNA methylation, inhibiting expression of DNA demethylases, and retargeting of histone H3K9 methylation act in a stochastic and uncoordinated fashion. As a result, new and aberrant epigenetic patterns were progressively formed over several plant generations in the absence of mCG. Interestingly, the unconventional redistribution of epigenetic marks was necessary to ârescueâ the loss of mCG, since mutant plants impaired in rescue activities were severely dwarfed and sterile. Our results provide evidence that mCG is a central coordinator of epigenetic memory that secures stable transgenerational inheritance in plants. Experiment Overall Design: Per entry, two biological replicates of leaf tissue (approx. 12th true leaf) from 9-12 plants were frozen in liquid nitrogen. DNA was CTAB extracted and isopropanol precipitated, RNase A and Proteinase K treated, re-extracted and ethanol precipitated. Two replicate 3 µg genomic DNA samples of 2nd generation met1-3, 4th generation met1-3 and Col-0 were sheared by sonication and methylated DNA was immunoprecipitated, as previously described (Weber et al., 2005), and amplified following the chromatin immunoprecipitation assay protocol (Affymetrix). Two replicates per entry with 7.5 µg DNA were fragmented; end labeled, and hybridized on Affymetrix ATH1 arrays as recommended (Affymetrix). Microarray data analysis was performed using the following procedure. First, background adjustments were made using the gcRMA method available in the Bioconductor package of R. Next, background-adjusted values from the six ATH1 datasets were quantile normalized and average signal intensities were determined in log2 scale per probe set. Experiment Overall Design: Contrast coefficient ratios for all pair-wise comparisons were calculated as follows: met1-3 2nd/Col-0, met1-3 4th/Col-0, and met1-3 4th/met1-3 2nd. Corrections for multiple comparisons at the 5% false discovery rate (FDR) were performed and significant differences were detected using Fisherâs test. Contrast coefficient ratios and p values may be found in the Supplementary file at the foot of this record. For each probe set, three outcomes (significantly hypermethylated, no difference, and significantly hypomethylated) were possible per comparison, creating 27 possible methylation profiles analyzed at the 5% FDR level.
2008-06-16 | E-GEOD-8279 | biostudies-arrayexpress
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