Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE21673
PROVIDER: PRJNA129349 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Relationship between nucleosome positioning and DNA methylation: Bisulfite-Seq, ChIP-Seq, and Mnase-Seq
| PRJNA129325 | ENA
Project description:Arabidopsis Root Methylation and Root Nucleosome Positioning
| PRJNA237956 | ENA
Project description:Determinants of nucleosome positioning and their influence on plant gene expression
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Project description:Interdependence between DNA methylation and transcription
| PRJNA97449 | ENA
Project description:Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer1, 2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. We also found that DNA methylation enriched on exons, consistent with the targeting of DNA methylation to nucleosomes. Genomic DNA associated with RNAP II was isolated by ChIP using an anti-PolII antibody.
2010-05-28 | E-GEOD-21818 | biostudies-arrayexpress
Project description:Global Nucleosome Positioning in Arabidopsis using whole genome Tiling Microarray
| PRJNA134271 | ENA
Project description:Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. We also found that DNA methylation enriched on exons, consistent with the targeting of DNA methylation to nucleosomes. Genomic DNA from Arabidopsis thaliana was MNase digested, size selected and sequenced. Genomic DNA associated with H3 was isolated using ChIP and sequenced. Genomic DNA from human HSF1 embryonic stem cells was bisulfite converted and sequenced.
2010-05-29 | E-GEOD-21821 | biostudies-arrayexpress
Project description:DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions, that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule and thus, single cell level that can be used to monitor disease progression and response to therapy.
2012-09-12 | GSE40770 | GEO
Project description:We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing.
2023-04-06 | GSE148173 | GEO