Variation in DNA methylation patterns more common among maize inbreds than among tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE38503 | GEO | 2012/08/27
SECONDARY ACCESSION(S): PRJNA168024
REPOSITORIES: GEO
Similar Datasets
Project description:Epigenetic marks such as DNA methylation can act as heritable marks on a genome leading to unique regulation of genomic sequences. As a transient mark, DNA methylation has been identified as a possible mechanism for reversible genetic regulation of cells derived through either mitotic or meiotic cellular division. Although variation between epigenetic states is known to exist between individuals, there is little known about the variability of DNA methylation patterns between different developmental stages of an individual. We have assessed genome-wide DNA methylation patterns in four tissues of two inbred maize lines: B73 and Mo17. Although hundreds of regions of differential methylation are present between the two genotypes, few examples of tissue-specific DNA methylation variation were observed. The lack of clear epigenetic variation between tissues indicates the limited impact of DNA methylation on developmental processes within maize. meDIP-chip analysis of four maize tissues identifed few tissue-specific DNA methylation variable regions (tDMRs), whereas hundreds of genotype-specific DMRs were identified that were conserved across tissues. Methylation profiles for tassel, embryo, endosperm, and leaf of the maize inbred lines B73 and Mo17. Three biological replications for each tissue of each genotype were performed. A custom 2.1M NimbleGen array (GPL13499) was used for embryo, endosperm, and leaf, and a custom 3x1.4M NimbleGen array containing a subset of probes from the 2.1M NimbleGen array (GPL15621) was used for tassel. All of the processed data is based on the largest number of comparable probes (~1.4M) between the two arrays.
2012-08-27 | E-GEOD-38503 | biostudies-arrayexpress
Project description:Cellular differentiation involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. Using Differential Methylation Hybridization (DMH) in combination with a custom DMH array containing more than 53,000 features covering more than 16,000 murine genes, we carried out a genome-wide screen for cell- and tissue-specific differentially methylated regions (tDMRs) in undifferentiated embryonic stem cells (ESCs), in in-vitro induced neural stem cells (NSCs) and 8 differentiated embryonic and adult tissues. Unsupervised clustering of the generated data showed distinct cell- and tissue-specific DNA methylation profiles, revealing 202 significant tDMRs (p<0.005) between ESCs and NSCs and a further 380 tDMRs (p<0.05) between NSCs/ESCs and embryonic brain tissue. We validated these tDMRs using direct bisulfite sequencing (DBS) and methylated DNA immunoprecipitation on chip (MeDIP-chip). Gene ontology (GO) analysis of the genes associated with these tDMRs showed significant (absolute Z score >1.96) enrichment for genes involved in neural differentiation, including e.g. Jag1 and Tcf4. Our results provide robust evidence for the relevance of DNA methylation in early neural development and identify novel marker candidates for neural cell differentiation.
2012-03-22 | E-MTAB-576 | biostudies-arrayexpress
Project description:DNA methylation is one of the important epigenetic marks conserved across both plants and animals. Recent work in Arabidopsis thaliana has demonstrated the existence of large geographic variation in DNA methylation, which must reflect genetic differences and/or an epigenetic memory of local environments. Here we investigate the cause of these differences in a genetic cross between a southern Swedish line with low DNA methylation and a northern Swedish line with high DNA methylation, carried out at two different temperatures. Using bisulfite-sequencing data with nucleotide-level resolution on hundreds of individuals, we find genetic and environmental factors regulating DNA methylation variation.
2022-12-31 | GSE215839 | GEO
Project description:There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. In many EWASs, it is not possible to analyze the target tissue in large numbers of live humans, and consequently surrogate tissues are employed, most commonly blood. But there is as yet no evidence demonstrating that blood is more informative than buccal cells, the other easily accessible tissue. To assess the potential of buccal cells for use in EWASs, we performed a comprehensive analysis of a buccal cell methylome using whole-genome bisulfite sequencing. Strikingly, a buccal vs. blood comparison reveals >6X as many hypomethylated regions in buccal. These tissue-specific differentially methylated regions (tDMRs) are strongly enriched for DNaseI hotspots. Almost 75% of these tDMRs are not captured by commonly used DNA methylome profiling platforms such as Reduced Representational Bisulfite Sequencing and the Illumina Infinium HumanMethylation450 BeadChip, and they also display distinct genomic properties. Buccal hypo-tDMRs show a statistically significant enrichment near SNPs associated to disease identified through GWASs. Finally, we find that, compared with blood, buccal hypo-tDMRs show significantly greater overlap with hypomethylated regions in other tissues. We propose that for non-blood based diseases/phenotypes, buccal will be a more informative tissue for EWASs. Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2013-03-28 | E-GEOD-45529 | biostudies-arrayexpress
Project description:There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. In many EWASs, it is not possible to analyze the target tissue in large numbers of live humans, and consequently surrogate tissues are employed, most commonly blood. But there is as yet no evidence demonstrating that blood is more informative than buccal cells, the other easily accessible tissue. To assess the potential of buccal cells for use in EWASs, we performed a comprehensive analysis of a buccal cell methylome using whole-genome bisulfite sequencing. Strikingly, a buccal vs. blood comparison reveals >6X as many hypomethylated regions in buccal. These tissue-specific differentially methylated regions (tDMRs) are strongly enriched for DNaseI hotspots. Almost 75% of these tDMRs are not captured by commonly used DNA methylome profiling platforms such as Reduced Representational Bisulfite Sequencing and the Illumina Infinium HumanMethylation450 BeadChip, and they also display distinct genomic properties. Buccal hypo-tDMRs show a statistically significant enrichment near SNPs associated to disease identified through GWASs. Finally, we find that, compared with blood, buccal hypo-tDMRs show significantly greater overlap with hypomethylated regions in other tissues. We propose that for non-blood based diseases/phenotypes, buccal will be a more informative tissue for EWASs. Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2013-05-02 | E-GEOD-46573 | biostudies-arrayexpress
Project description:Background DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific Differentially Methylated Regions (tDMRs) in Illumina 450k chip data on four peripheral (blood, saliva, buccal swab and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum, spleen with matched blood samples). Results The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with that in blood for a subset of CpG sites in a locus and tissue-specific manner. Conclusions We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that are marked by DNA methylation measured in easy accessible peripheral tissues.
2013-08-06 | GSE48472 | GEO
Project description:DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, other genetic changes such as transposon insertions also can lead to changes in DNA methylation levels. Genome-wide profiles of DNA methylation levels for 20 maize inbreds were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize genotypes resulting in the discovery of 1,966 common DMRs and 1,754 rare DMRs. Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with SNPs found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the DNA methylation variation. The analysis of gene expression in the same samples used for DNA methylation profiling identifies over 300 genes with expression patterns that are significantly associated with the DNA methylation variation among genotypes. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic variation is often stably inherited and can influence expression level of genes in the population. Methylation profiles in seedling tissue of a panel of 51 maize inbred lines using a custom 2.1M or 1.4M feature NimbleGen array. Methylation profiles in seedling tissue of maize inbred lines, teosinte and recombinant inbred lines (RILs) derived from B73 and Mo17 using a custom 12x270K NimbleGen array. Inbred lines B73 and Mo17 each had 3 biological replicates, the other sample had 1 replicate.
2013-08-12 | E-GEOD-46949 | biostudies-arrayexpress
Project description:Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. Methylation of cytosine residues provides a mechanism for the inheritance of epigenetic information. We have profiled the distribution of DNA methylation in the large, complex genome of Zea mays (ssp. mays). DNA methylation levels are higher near the centromeres and are generally inversely correlated with recombination and gene expression levels. However, genes that are located in non-syntenic genomic positions relative to species related closely to maize exhibit higher levels of DNA methylation independent of expression state. A comparison of the DNA methylation levels in two different inbred genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions. The regions of differential methylation in B73 and Mo17 often occur in intergenic regions but some of these regions are located within or near genes. There is evidence that variation in DNA methylation levels can occur in genomic regions that are identical-by-descent, illustrating the potential for epigenetic variation that is not tightly linked to genetic changes. A comparison of the genotype and epigenotype in a panel of near-isogenic lines reveals evidence for epigenetic variation that is conditioned by linked regions as well as examples of epigenetic variation that is conditioned by unlinked genomic regions. Our many examples of epigenetic variation, including some without tightly linked genetic variation, have implications for plant breeding and for natural selection. Methylation profiles in seedling tissue of the maize inbred lines B73 and Mo17. Each genotype was compared for three biological replications using a gene-focused custom 2.1M NimbleGen array.
2011-11-21 | E-GEOD-29099 | biostudies-arrayexpress
Project description:Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. To begin to understand the impact of natural variation on histone methylation levels we generated and quantified large-scale genome-wide ChIP-seq data in a panel of rat recombinant inbred strains and their parental progenitors. Linkage analysis identified hundreds of cis- and trans-acting loci responsible for quantitative differences in histone trimethyl-lysine levels in left ventricular heart and liver tissues. We assessed the association of histone methylation and gene expression levels by generating deep RNA-seq profiles across the segregating population. Among the main findings, causal modelling of DNA variation together with histone methylation and gene expression levels enhanced the prediction of gene expression traits (eQTLs) by ~20%. Moreover, allele specific differences of histone trimethyl-lysine levels at alternative promoters were associated with differential usage of transcriptional start sites. Our data suggest that genetic variation has widespread impact on histone modifications. The highly adapted interplay between DNA variation and chromatin structure has consequences on gene and isoform expression as direct functional outcome and demonstrated new avenues to find novel genotype Ð phenotype relationships. NOTE: Additional processed data files were added to this experiment on the 24th April 2014. They are in the zip archive E-MTAB-1102.additional.1.zip which is available under the 'Click to browse all available files' link.
2012-05-30 | E-MTAB-1102 | biostudies-arrayexpress
Project description:There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. In many EWASs, it is not possible to analyze the target tissue in large numbers of live humans, and consequently surrogate tissues are employed, most commonly blood. But there is as yet no evidence demonstrating that blood is more informative than buccal cells, the other easily accessible tissue. To assess the potential of buccal cells for use in EWASs, we performed a comprehensive analysis of a buccal cell methylome using whole-genome bisulfite sequencing. Strikingly, a buccal vs. blood comparison reveals >6X as many hypomethylated regions in buccal. These tissue-specific differentially methylated regions (tDMRs) are strongly enriched for DNaseI hotspots. Almost 75% of these tDMRs are not captured by commonly used DNA methylome profiling platforms such as Reduced Representational Bisulfite Sequencing and the Illumina Infinium HumanMethylation450 BeadChip, and they also display distinct genomic properties. Buccal hypo-tDMRs show a statistically significant enrichment near SNPs associated to disease identified through GWASs. Finally, we find that, compared with blood, buccal hypo-tDMRs show significantly greater overlap with hypomethylated regions in other tissues. We propose that for non-blood based diseases/phenotypes, buccal will be a more informative tissue for EWASs.
2013-05-02 | GSE46573 | GEO