Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE61457 | GEO | 2015/05/27
SECONDARY ACCESSION(S): PRJNA261158
REPOSITORIES: GEO
Similar Datasets
Project description:We generated base-resolution DNA methylomes of a series of DNMT knockout (KO) ES cells with improved coverage at highly repetitive elements. We find that DNMT1- and DNMT3a/3b-dependent activities actually work complementarily and simultaneously to establish symmetric CG methylation and CHH (H=A, T or C) methylation, and unexpectedly have “division of labor” to suppress retrotransposon long terminal repeats (LTRs) and long interspersed elements (LINEs), respectively. Our data also reveal CG density number of 30 seems like a 'threshold' to predetermine the level of methylation in wild type cells and the magnitude of methylation reduction in KO cells. Only genes with low CG number are either induced or surprisingly suppressed in hypomethylated genome. Our data unveil the concerted action of DNMT enzymes in the establishment/maintenance of methylation patterns. Genomic DNA from four different cell lines were treated with bisulfite and sequenced with the Illumina HiSeq platform using paired end reads.
2015-05-27 | E-GEOD-61457 | biostudies-arrayexpress
Project description:Cytosine methylation silences transposable elements in plants, vertebrates and fungi, but also regulates gene expression1. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C or T) and CHH, with CHH methylation targeted by the RNA interference (RNAi) pathway2. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation3. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, while CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data demonstrate that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops. Keywords: Epigenetics Examination of DNA methylation in rice
2010-11-01 | E-GEOD-22591 | biostudies-arrayexpress
Project description:OsDDM1 and OsDRM2 display functional specificities that define distinct DNA methylation pathways in the bulk of DNA methylation of the rice genome Cr_DJ.CG.bw: Cr_DJ CG methylation Cr_DJ.CHG.bw: Cr_DJ CHG methylation Cr_DJ.CHH.bw: Cr_DJ CHH methylation ddm1ab.CG.bw: ddm1a/1b CG methylation ddm1ab.CHG.bw: ddm1a/1b CHG methylation ddm1ab.CHH.bw: ddm1a/1b CHH methylation S706.CG.bw: osdrm2 CG methylation S706.CHG.bw: osdrm2 CHG methylation S706.CHH.bw: osdrm2 CHH methylation H3k9me2_macs_peaks.xls: CrDJ H3K9me2 modification peaks H3k9me2_macs_treat_afterfiting.wig: CrDJ H3K9me2 modification wig CrDJ_K27_macs_peaks.xls: CrDJ H3K27me3 modification peaks CrDJ_K27_macs_treat_afterfiting.wig: CrDJ H3K27me3 modification wig DJvsddm1a1b_DESeq2_treated_results.xls: CrDJ and osddm1a1b different expression genes DJvsS706_DEseq2_treated.results.xls: CrDJ and osdrm2 different expression genes smRNA24nt.gff: CrDJ 24nt smRNA smRNA24nt.706.gff: osdrm2 24nt smRNA
2016-06-13 | E-GEOD-81436 | biostudies-arrayexpress
Project description:Cytosine methylation silences transposable elements in plants, vertebrates and fungi, but also regulates gene expression1. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C or T) and CHH, with CHH methylation targeted by the RNA interference (RNAi) pathway2. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation3. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, while CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data demonstrate that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops. Keywords: Epigenetics
2010-11-01 | GSE22591 | GEO
Project description:5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, while mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, while mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small-interfering RNAs and H3K9me2, without gaining CHH methylation. This suggests that spontaneous epialelles that arise in plant cell cultures are stably maintained by small RNA independently of the canonical RNA-directed DNA methylation pathway. In contrast, loci that fail to produce siRNA are targeted for demethylation when cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.
2020-12-03 | GSE157670 | GEO
Project description:5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, while mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, while mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small-interfering RNAs and H3K9me2, without gaining CHH methylation. This suggests that spontaneous epialelles that arise in plant cell cultures are stably maintained by small RNA independently of the canonical RNA-directed DNA methylation pathway. In contrast, loci that fail to produce siRNA are targeted for demethylation when cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.
2020-12-03 | GSE155958 | GEO
Project description:5-methyl cytosine in plant genomes occurs in all sequence contexts, especially in heterochromatin, transposons and other repeats. During replication, nascent cytosines in symmetric contexts (CG) are guided for methylation by hemi-methyl C on the parental DNA strands of both daughter chromatids. However nascent cytosines in the asymmetric CHH context or in symmetric CHG (where H=A, T or C) use modified histones and 24-nt small interfering RNAs to restore methylation to each daughter chromatid. Here, we use fluorescent activated sorting of EdU-labeled nuclei to examine DNA methylation dynamics in dividing cell cultures of Arabidopsis thaliana. We find that CG methylation becomes transiently asymmetric during late S phase, but is rapidly restored during each cell division, while CHG methylation remains asymmetric and is substantially reduced. Levels of mCHH are extremely low in dividing cells, accompanied by a shift from 24-nt to 21-nt epigenetically activated small RNAs (easiRNAs) and a loss of histone lysine-9 methylation. When cell division arrests, RNA-directed CHH methylation is restored, but only at loci that retained 24-nt siRNAs. Comparisons with methylation patterns in pollen suggest that DNA methylation reprogramming in microspores (G2), sperm cells (S phase) and the vegetative nucleus (which is quiescent) reflect their cell cycle stage. Our results also account for the loss of non-CG methylation in plants micropropagated as clones, which undergo methylation reprogramming in the absence of fertilization.
2020-12-03 | GSE117316 | GEO
Project description:5-methyl cytosine in plant genomes occurs in all sequence contexts, especially in heterochromatin, transposons and other repeats. During replication, nascent cytosines in symmetric contexts (CG) are guided for methylation by hemi-methyl C on the parental DNA strands of both daughter chromatids. However nascent cytosines in the asymmetric CHH context or in symmetric CHG (where H=A, T or C) use modified histones and 24-nt small interfering RNAs to restore methylation to each daughter chromatid. Here, we use fluorescent activated sorting of EdU-labeled nuclei to examine DNA methylation dynamics in dividing cell cultures of Arabidopsis thaliana. We find that CG methylation becomes transiently asymmetric during late S phase, but is rapidly restored during each cell division, while CHG methylation remains asymmetric and is substantially reduced. Levels of mCHH are extremely low in dividing cells, accompanied by a shift from 24-nt to 21-nt epigenetically activated small RNAs (easiRNAs) and a loss of histone lysine-9 methylation. When cell division arrests, RNA-directed CHH methylation is restored, but only at loci that retained 24-nt siRNAs. Comparisons with methylation patterns in pollen suggest that DNA methylation reprogramming in microspores (G2), sperm cells (S phase) and the vegetative nucleus (which is quiescent) reflect their cell cycle stage. Our results also account for the loss of non-CG methylation in plants micropropagated as clones, which undergo methylation reprogramming in the absence of fertilization.
2020-12-03 | GSE117315 | GEO
Project description:Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of siRNA-targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo. Keywords: Epigenetics; bisulfite sequencing Examination of DNA methylation in four Arabidopsis tissues Description of processed data and raw data file contents can be found in the attached README.txt file
2009-06-16 | E-GEOD-15922 | biostudies-arrayexpress
Project description:We uncover distinct DNA methylation dynamics over genes and repeat sequences during early plant life in Arabidopsis. While gene body methylation, which is restricted to CG sites and concerns 20-30% of all genes is detected at all stages examined, it typically fluctuates over a few CGs, with no coherent pattern. In contrast, transposable elements and their relics as well as other repeat sequences, have consistently high methylation levels at CGs and show increasing CHG and especially CHH methylation during embryogenesis. Remarkably, methylation reaches 100% at many individual CHH sites in the mature embryo, compared to the 10-20% methylation usually observed at CHH sites in seedlings or adult plants. Moreover, the progressive increase in CHG and CHH methylation in embryos mirrors the loss of DNA methylation at CG and CHG sites in the endosperm, suggesting transfer of information from the endosperm to the embryo, presumably in the form of small RNAs. Finally, impairing the embryo to seedling transition through loss of PRC2 activity results in the persistence of high CHH methylation levels after germination and specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. Collectively, our findings indicate a lack of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in targeting DNA methylation to transposable element and other repeat sequences in all cells of the mature embryo.
2017-08-23 | GSE85975 | GEO