High Resolution Mapping and Functional Analysis of the Methylome in Arabidopsis (mCIP, MBD)
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE5094 | GEO | 2006/08/30
SECONDARY ACCESSION(S): PRJNA95343
REPOSITORIES: GEO
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Project description:Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. Unexpectedly, over one third of expressed genes contained methylation within transcribed regions, whereas only ~5% of genes contained methylation within promoter regions. Interestingly, genes methylated in transcribed regions were highly expressed and constitutively active, whereas promoter-methylated genes showed a greater degree of tissue-specific expression. Analysis of several DNA methyltransferase mutants revealed widespread epigenetic regulation of protein-coding genes as well as non-coding RNA genes of unknown function. Keywords: whole genome profiling, poly(A)RNA, DNA methylation
2006-08-17 | GSE5074 | GEO
Project description:Integration of the bacterial T-DNA into the plant genome by virulent agrobacteria causes crown gall development on many plant species. Plant tumor development shares fundamental similarities with mammalian cancer progression despite obvious differences in initiation of tumor development. For neoplastic growth in mammals, DNA methylation changes are known to be essential. The role of epigenetic modifications for plant tumor development is addressed here. Genome-wide comparison of methylation profiles of Arabidopsis crown galls and tumor-free tissue revealed 2,876 annotated genes that were affected by differential methylation. Thereof, 1,822 genes were hit by hypermethylated regions and 1,100 genes overlapped with hypomethylated regions (sum of hyper-and hypomethylated genes is higher than the number of affected genes because one gene may contain several differentially methylated regions [DMRs]). DMRs found to be methylated only in tumor-free tissue covered 275 kb of the genome, whereas those methylated only in crown galls total to 560 kb. Contrary to the globally hypermethylated tumor genome, promoter regions of protein coding genes appeared to be rather hypomethylated. In contrast, mammalian cancer cells are associated with global hypomethylation and local hypermethylation of gene promoters. In summary, while aberrant DNA methylation in mammals increases malignacy of the cancer phenotype, our results indicate that methylation events in the plant genome rather confine tumor growth. All 15,431 mCIP-enriched regions reported in the paper are contained in the supplementary BED files. mCIP of gDNA from crown galls vs. mCIP of gDNA from inflorescence stalks (3 biol. replicates each)
2013-02-18 | E-GEOD-37680 | biostudies-arrayexpress
Project description:Integration of the bacterial T-DNA into the plant genome by virulent agrobacteria causes crown gall development on many plant species. Plant tumor development shares fundamental similarities with mammalian cancer progression despite obvious differences in initiation of tumor development. For neoplastic growth in mammals, DNA methylation changes are known to be essential. The role of epigenetic modifications for plant tumor development is addressed here. Genome-wide comparison of methylation profiles of Arabidopsis crown galls and tumor-free tissue revealed 2,876 annotated genes that were affected by differential methylation. Thereof, 1,822 genes were hit by hypermethylated regions and 1,100 genes overlapped with hypomethylated regions (sum of hyper-and hypomethylated genes is higher than the number of affected genes because one gene may contain several differentially methylated regions [DMRs]). DMRs found to be methylated only in tumor-free tissue covered 275 kb of the genome, whereas those methylated only in crown galls total to 560 kb. Contrary to the globally hypermethylated tumor genome, promoter regions of protein coding genes appeared to be rather hypomethylated. In contrast, mammalian cancer cells are associated with global hypomethylation and local hypermethylation of gene promoters. In summary, while aberrant DNA methylation in mammals increases malignacy of the cancer phenotype, our results indicate that methylation events in the plant genome rather confine tumor growth. All 15,431 mCIP-enriched regions reported in the paper are contained in the supplementary BED files.
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Project description:We have previously developed an approach that fractionates genomic DNA fragments depending on their CpG density (methyl-CpG-immunoprecipitation, MCIp), and adapted this approach to identify regions that are differentially methylated in the two closely related regulatory T-cells (Treg cells) and conventional T-cells (Tconv cells). Because Treg cells naturally occur at a relatively low frequency, we used a previously established protocol to expand Treg cells from a stable naïve Treg population that is characterized by the co-expression of CD4, CD25 and CD45RA. We separated gDNA of both expanded T cell lineages (Tregexp and Tconvexp) into unmethylated (CpG) and methylated pools (mCpG) using MCIp and compared cell type-specific differences in DNA methylation by co-hybridization of the two umethylated or the two methylated DNA subpopulations of Treg and Tconv, respectively, to these locus-wide custom tiling arrays. As enriched DNA-fragments from a cell type in the methylated fraction should be depleted in the unmethylated fraction, the signal intensities in CpG pool and mCpG pool hybridizations should complement themselves (“Mirror-Image” approach) and thereby allow the identification of differentially methylated regions (DMR). Because we expected to find lineage-specific methylation differences with greater probability in regions associated with differential transcriptional activity, we limited our analysis to gene loci that showed cell type-specific gene expression in Treg versus Tconv cells plus a handful of control regions that were equally expressed in both cell types. The microarray used in this study covered 12 megabases of the human genome and contained 69 regions (with a median size of 100.000 kb) and 128 proximal promoter regions and 181 genes, which included a number of well known and functionally relevant genes like CD40LG, IFNG, FOXP3, IL2RA and CTLA4. Keywords: MCIp-on-chip; comparative genomic hybridization
2009-05-20 | GSE14233 | GEO
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2010-06-05 | E-GEOD-17512 | biostudies-arrayexpress
Project description:DNA-methylation is a vital epigenetic mark that participates in establishing and maintaining chromatin structures and in regulating gene transcription during mammalian development and cellular differentiation. Inter-individual differences in methylation patterns may represent a major source of phenotypic variation, however, the determinants, inheritance, extent, and consequences of such differences are poorly understood. Here we have analysed methylation profiles of immune cells from two inbreed mouse strains (C57BL/6 & BALB/c) that represent prototypic models for Th1- or Th2-dominated immune responses. Using a methyl-CpG immunoprecipitation approach, genomes were fractionated into methylated and unmethylated genome pools and separately analysed at 180 genomic regions (covering 28 Mb of the mouse genome) that were selected based on differential gene expression between both mouse strains. Differentially methylated regions are detected by analyzing array probes for diametrically opposed enrichment behaviour between both hybridizations (e.g. a region that is relatively enriched in the unmethylated pool of BALB/c and shows reverse enrichment behaviour in the methylated pool is considered hypomethylated in BALB/c). The integrated analysis of hypo and hypermethylation profiles allowed the identification of several hundred differentially methylated regions, but also uncovered regions that were duplicated in one strain, contained single nucleotide polymorphisms or micro- and macro-deletions. Keywords: MCIp-on-Chip; comparative genomic hybridization Methylation profiles of regions, harbouring differentially expressed genes in BMM, were compared between C57BL/6 and BALB/c. Two independently grown, harvested and MCIp treated gDNA preparations were used for each mouse strain (Two biological replicates; One replicate per array). Hypo- and hypermethylated pools serve as diametrically oposed technical replicates (mirror approach).
2010-05-15 | E-GEOD-14463 | biostudies-arrayexpress
Project description:To globally define methylation-âproneâ and -âprotectedâ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in eight acute leukemia samples as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. Keywords: MCIp-on-Chip; comparative genomic hybridization CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from leukemia samples was compared to the enriched material from normal blood monocytes to identify aberrantly methylated regions. Three biological replicates were analysed for each cell line.
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Project description:To globally define methylation-âproneâ and -âprotectedâ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in two acute leukemia cell lines as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. Keywords: MCIp-on-Chip; comparative genomic hybridization CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from leukemia cell lines was compared to the enriched material from normal blood monocytes to identify aberrantly methylated regions. Three biological replicates were analysed for each cell line.
2010-06-05 | E-GEOD-17455 | biostudies-arrayexpress