Non-CG methylation is more potent than CG methylation in moss genome regulation [Athaliana RNA-Seq]
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE142052 | GEO | 2020/12/30
REPOSITORIES: GEO
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Project description:Cytosine methylation is commonly targeted to symmetrical CG sites, as well as to non-CGs, such as the symmetrical-CHG and asymmetric-CHH sites in plants (H= A, C or T). Thus far, depletion of CG methylation in plants was associated with ample transcriptional activation of transposons. Here, we profiled transcription in various context specific methylation mutants in the early-diverged plant, Physcomitrella patens. We discovered that specific elimination of CG methylation is fully complemented by non-CG methylation but not vice versa. Between the symmetrically-methylated sites, CHG methylation silenced transposons stronger than CG methylation did. Finally, non-CG methylation revealed as crucial for the silencing of CG depleted transposons. Our results suggest that non-CG methylation evolved to silence transposons due to functional limitations and/or rapid mutability of methylated-CGs.
2020-12-30 | GSE142053 | GEO
Project description:Cytosine methylation is commonly targeted to symmetrical CG sites, as well as to non-CGs, such as the symmetrical-CHG and asymmetric-CHH sites in plants (H= A, C or T). Thus far, depletion of CG methylation in plants was associated with ample transcriptional activation of transposons. Here, we profiled transcription in various context specific methylation mutants in the early-diverged plant, Physcomitrella patens. We discovered that specific elimination of CG methylation is fully complemented by non-CG methylation but not vice versa. Between the symmetrically-methylated sites, CHG methylation silenced transposons stronger than CG methylation did. Finally, non-CG methylation revealed as crucial for the silencing of CG depleted transposons. Our results suggest that non-CG methylation evolved to silence transposons due to functional limitations and/or rapid mutability of methylated-CGs.
2020-12-30 | GSE142051 | GEO
Project description:H3K27me3 is a repressive chromatin mark of genes and is catalyzed by homologs of Enhancer of zeste [E(z)], a component of Polycomb-repressive complex 2 (PRC2), while DNA methylation that occurs in CG and non-CG (CHG and CHH, where H is A, C or T) contexts is a hallmark of transposon silencing in plants. However, relationship between H3K27me3 and DNA methylation in gene repression remains unclear. In addition, the mechanism of PRC2 recruitment to specific genes is not known in plants. Here, we show that SDG711, a rice E(z) homolog, is required to maintain H3K27me3 of many developmental genes after shoot meristem to leaf transition and that many H3K27me3-marked developmental genes are also methylated at non-CG sites in the body regions. SDG711-binding and SDG711-mediated ectopic H3K27me3 also target genes methylated at non-CG sites. Conversely, mutation of OsDRM2, a major rice CHH methyltransferase, resulted in loss of SDG711-binding and H3K27me3 from many genes and their de-repression. Furthermore, we show that SDG711 physically interacts with OsDRM2 and a putative CHG methylation-binding protein. These results together suggest that the repression of many developmental genes may involve both DRM2-mediated non-CG methylation and PRC2-mediated H3K27me3 and that the two marks are not generally mutually exclusive but may cooperate in repression of developmentally regulated genes in rice.
2016-12-18 | GSE71640 | GEO
Project description:Allele specific DNA methylation (ASM) is crucial for genomic imprinting and mammalian development. Here we present a base-resolution, genome-wide allelic DNA methylation map for both CG and non-CG sites in the mouse brain. We found parent-of-origin dependent (imprinted) ASM at 1,952 CGs which form 55 discrete clusters. This uncovers 31 reported differentially methylated regions (DMRs), including virtually all known germline DMRs, and 24 novel candidate DMRs with some occurring at microRNA genes. In the same adult tissue we also report a surprising presence of non-CG methylation with some showing evidence of imprinting. Finally, we identified sequence dependent ASM at 131,765 CGs. Interestingly, methylation at these sites exhibits a strong dependence on the immediate adjacent bases, allowing us to define a conserved sequence preference for the mammalian DNA methylation machinery. Our genome-wide ASM map should help with understanding the epigenetic differences between two parental genomes in mammals. The crosses of the two mouse strains 129x1/SvJ (129) and Cast/EiJ (Cast) were performed at Jackson Laboratories (http://jaxmice.jax.org/) and the male mice F1 offspring and males of each of the two parental strains were shipped to investigator laboratories at 8 to 9 weeks of age. A total of 500ng genomic DNA isolated from IMR90, MEF, and the frontal cortex of F1i and F1r was digested in parallel by the DNA methylation dependent restriction enzyme FspEI. FspEI recognizes the CmC site (the second cytosine is methylated and can be in the context of CG, CHG or CHH) and creates a 5 protruding end 17 bases downstream of the methylcytosine. A similar experiment was performed by incubating the F1i genomic DNA with a DNA methylation independent restriction enzyme BstNI. The digested DNA was gel purified, size selected for fragments within 100-600bp. The resulting DNA was then prepared as genomic DNA libraries for high-throughput sequencing (Illumina).
2012-02-15 | E-GEOD-33579 | biostudies-arrayexpress
Project description:As a key epigenetic modification, DNA methylation is essential for normal development by regulating processes like gene expression, genomic imprinting, and suppression of repetitive elements. However, DNA methylation in the cattle genome is not well understood. Here we presented the first single-base-resolution maps of DNA methylation in 10 diversely somatic tissues harvested from the sequenced Hereford cow L1 Dominette 01449 and her relatives using reduced representation bisulphite sequencing (RRBS). In total, we observed 1,868,049 high accuracy cytosines that located in the CG enriched regions. Similar to the methylation patterning in other species, the CG context was predominant methylated. Widespread differences were identified between the methylation patterns of CG and non-CG contexts. They were distributed differentially among the genomic features, including the genic regions, CpG islands, and repetitive sequences. Autocorrelation analysis among adjacent residues illustrated that methylation level of CGs were highly correlated in a region. In contrast, weak or no correlation was found among non-CGs or between CGs and non-CGs. The distinct distribution and low correlation of CG and non-CG methylation suggested that non-CG methylation may be independent from CG methylation and may be mediated by different mechanisms. We also detected 798 tissue-specific differentially methylated cytosines (tDMC) and 131 tissue-specific differentially methylated CpG islands. Combined analysis with the RNA-seq data, we discovered several non-CGs in tDMCs also highly correlated with gene expression, which implied the potential function of non-CG methylation in somatic cells in addition to pluripotent cells. In summary, we showed that non-CGs exist in bovine tissues and some of them were correlated with tissue-specific functions. This study provided essential information for the cytosine methylation patterning in bovine somatic tissues.
2017-02-14 | GSE86323 | GEO
Project description:As a key epigenetic modification, DNA methylation is essential for normal development by regulating processes like gene expression, genomic imprinting, and suppression of repetitive elements. However, DNA methylation in the cattle genome is not well understood. Here we presented the first single-base-resolution maps of DNA methylation in 10 diversely somatic tissues harvested from the sequenced Hereford cow L1 Dominette 01449 and her relatives using reduced representation bisulphite sequencing (RRBS). In total, we observed 1,868,049 high accuracy cytosines that located in the CG enriched regions. Similar to the methylation patterning in other species, the CG context was predominant methylated. Widespread differences were identified between the methylation patterns of CG and non-CG contexts. They were distributed differentially among the genomic features, including the genic regions, CpG islands, and repetitive sequences. Autocorrelation analysis among adjacent residues illustrated that methylation level of CGs were highly correlated in a region. In contrast, weak or no correlation was found among non-CGs or between CGs and non-CGs. The distinct distribution and low correlation of CG and non-CG methylation suggested that non-CG methylation may be independent from CG methylation and may be mediated by different mechanisms. We also detected 798 tissue-specific differentially methylated cytosines (tDMC) and 131 tissue-specific differentially methylated CpG islands. Combined analysis with the RNA-seq data, we discovered several non-CGs in tDMCs also highly correlated with gene expression, which implied the potential function of non-CG methylation in somatic cells in addition to pluripotent cells. In summary, we showed that non-CGs exist in bovine tissues and some of them were correlated with tissue-specific functions. This study provided essential information for the cytosine methylation patterning in bovine somatic tissues.
2017-02-14 | GSE76346 | GEO
Project description:CRISPR-based targeted modification of epigenetic marks is an important strategy to regulate the expression of genes and their associated phenotypes in plants and animals. The manipulation of DNA cytosine methylation is particularly attractive in plants since DNA methylation changes are often heritable in subsequent plant generations. Although plants have DNA methylation in all sequence contexts (CG, CHG, CHH, where H can be any nucleotide but G), methylation at symmetrical CG sites is the most important for gene silencing, and is also the most efficiently maintained through miotic and meiotic cell divisions. Thus, DNA methylation targeting tools that directly install CG methylation are highly desirable. Here we have developed two CRISPR-based CG specific targeted DNA methylation systems for plants using the DNA methyltransferase MQ1 (SssI) from the bacterium Mollicutes spiroplasma. To reduce off-target effects, we used a variant of the enzyme with reduced catalytic activity. We demonstrate that methylation added by MQ1 is highly target-specific and can be heritably maintained in the absence of the effector. These tools should be valuable both in crop engineering and in plant genetic research.
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Project description:Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints. DNA methylation, RNA and nucleosome sequencing data for diverse eukaryotes
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Project description:Allele specific DNA methylation (ASM) is crucial for genomic imprinting and mammalian development. Here we present a base-resolution, genome-wide allelic DNA methylation map for both CG and non-CG sites in the mouse brain. We found parent-of-origin dependent (imprinted) ASM at 1,952 CGs which form 55 discrete clusters. This uncovers 31 reported differentially methylated regions (DMRs), including virtually all known germline DMRs, and 24 novel candidate DMRs with some occurring at microRNA genes. In the same adult tissue we also report a surprising presence of non-CG methylation with some showing evidence of imprinting. Finally, we identified sequence dependent ASM at 131,765 CGs. Interestingly, methylation at these sites exhibits a strong dependence on the immediate adjacent bases, allowing us to define a conserved sequence preference for the mammalian DNA methylation machinery. Our genome-wide ASM map should help with understanding the epigenetic differences between two parental genomes in mammals.
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Project description:Allele specific DNA methylation (ASM) is crucial for genomic imprinting and mammalian development. Here we present a base-resolution, genome-wide allelic DNA methylation map for both CG and non-CG sites in the mouse brain. We found parent-of-origin dependent (imprinted) ASM at 1,952 CGs which form 55 discrete clusters. This uncovers 31 reported differentially methylated regions (DMRs), including virtually all known germline DMRs, and 24 novel candidate DMRs with some occurring at microRNA genes. In the same adult tissue we also report a surprising presence of non-CG methylation with some showing evidence of imprinting. Finally, we identified sequence dependent ASM at 131,765 CGs. Interestingly, methylation at these sites exhibits a strong dependence on the immediate adjacent bases, allowing us to define a conserved sequence preference for the mammalian DNA methylation machinery. Our genome-wide ASM map should help with understanding the epigenetic differences between two parental genomes in mammals.
2012-02-15 | GSE33579 | GEO