Identification and analysis of adenine N6-methylation sites in the rice genome
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ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE103145 | GEO | 2018/06/10
REPOSITORIES: GEO
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Project description:In mammalian cells, DNA methylation on the 5th position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N6-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, we identify a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylation of histone H3K4me2 and 6mA, and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data identify a novel DNA modification in C. elegans and raise the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes. SMRT-sequencing for a mixed cell population of wildtype worms 6mA ChIP-Seq for a mixed cell population of wildtype worms
2015-05-05 | E-GEOD-66504 | biostudies-arrayexpress
Project description:To interrogate single-base resolution 6mA sites in the genome-wide, we develop DA-6mA-seq (DpnI-Assisted N6-methylAdenine sequencing), an optimized sequencing method taking advantage of restriction enzyme DpnI, which exclusively cleaves methylated adenine sites. We find DpnI also recognizes other sequence motifs besides the canonical GATC restriction sites, largely expanding the application range of this method. DA-6mA-seq requires less starting material and lower sequencing depth than previous methods, but achieves higher sensitivity, providing a good strategy to identify 6mA in large genome with a low abundance of 6mA. We rebuild the 6mA maps of Chlamydomonas by DA-6mA-seq and then apply this method to another two eukaryotic organisms, Plasmodium and Penicillium. Further analysis reveals most 6mA sites are symmetric at various sequence contexts, suggesting 6mA may function as a new heritable epigenetic mark in eukaryotes. A new sequencing method is developed to detect 6mA in eukaryotes
2016-04-12 | E-GEOD-74430 | biostudies-arrayexpress
Project description:N6-methyldeoxyadenosine (6mA) is a newly-discovered DNA modification that plays a role in regulating plant adaptation to abiotic stresses. However, the changes and molecular regulatory mechanisms of N6-methyldeoxyadenosine under cold stress in plants remain uncertain. Here, we found the global level of 6mA in both Arabidopsis and rice are raised after cold treatment. Genome-wide profiling of 6mA revealed that 6mA peaks are primarily distributed within gene body regions under both normal and low-temperature conditions. Additionally, genes that were up-methylated were enriched in various biological processes, while down-methylated genes did not exhibit any significant enrichment. Association analysis showed that 6mA was positively correlated with gene expression level and 6mA-containing genes displayed a significantly higher expression level than non-6mA-containing genes. Joint analysis of the 6mA methylome and transcriptome of Arabidopsis and rice revealed that the fluctuations in 6mA levels caused by exposure to cold did not correlate with the changes of transcript levels in response to low temperatures. Moreover, we found that 6mA modified orthologous genes exhibit high expression levels. However, upon cold treatment, only a small amount of differentially 6mA-methylated orthologous genes were shared between Arabidopsis and rice. In sum, this study profiled the changes of 6mA in response to cold temperature and has unlocked the potential of this DNA modification in regulating the expression of stress-related genes.
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Project description:DNA methylation on N6-adenine (6mA) has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, its distribution patterns and potential functions in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana using single-molecule real-time sequencing. 6mA sites are widely distributed across the Arabidopsis genome and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA frequency positively correlates with the gene expression level in Arabidopsis. Consistently, histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, suggesting that 6mA serves as a novel epigenetic mark in land plants.
2018-04-16 | GSE107002 | GEO
Project description:DNA methylation on N6-adenine (6mA) has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, its distribution patterns and potential functions in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana using single-molecule real-time sequencing. 6mA sites are widely distributed across the Arabidopsis genome and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA frequency positively correlates with the gene expression level in Arabidopsis. Consistently, histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, suggesting that 6mA serves as a novel epigenetic mark in land plants.
2018-04-16 | GSE106962 | GEO
Project description:N6-methyldeoxyadenosine (6mA or m6dA), a well-known prokaryotic DNA modification has recently been shown to exist and play regulatory roles in eukaryotic genomic DNA. However, biological functions of 6mA in mammals remain to be explored largely due to its low abundance in most mammalian genomes. Here, we report a significant enrichment of 6mA in mammalian mitochondrial DNA (mtDNA), and identify METTL4 as a methyltransferase that installs 6mA. The level of 6mA in mtDNA is elevated up to over 0.02% of the total deoxyadenosines under hypoxia, representing ~7,00-fold enrichment over 6mA in the genomic DNA (gDNA) under normal growth conditions. The presence of 6mA negatively regulates mitochondrial transcription and balances mitochondrial function for cellular adaption to hypoxic stress. While DNA 5-methylcytosine (5mC) is a well-established, prevalent epigenetic mark in mammalian genomic DNA, our study reveals for the first time DNA 6mA methylation as a regulatory mark in mammalian mtDNA.
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Project description:DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we found that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also found that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.
2020-08-14 | PXD020608 | Pride
Project description:DNA methylation on N6-adenine (6mA), the most prevalent DNA modification in prokaryotes, has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, the distribution patterns and potential functions of 6mA in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genomes of Arabidopsis thaliana Columbia-0 (Col), using single-molecule real-time sequencing. DNA methylome analysis shows that 6mA sites are widely distributed across the Col genomes and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies with a trend of enrichment around the transcriptional start site. In addition to a common consensus 6mA site found in other eukaryotes, novel 6mA sites were found, indicating that 6mA could evolve new functions in land plants. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA positively correlates with the gene expression level in Col plants. Consistently, DNA affinity chromatography coupled with mass spectrometry reveals that histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, indicating that 6mA could serve as a potentially novel epigenetic mark in land plants.
2018-04-16 | GSE81594 | GEO
Project description:DNA methylation on N6-adenine (6mA), the most prevalent DNA modification in prokaryotes, has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, the distribution patterns and potential functions of 6mA in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genomes of Arabidopsis thaliana Columbia-0 (Col), using single-molecule real-time sequencing. DNA methylome analysis shows that 6mA sites are widely distributed across the Col genomes and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies with a trend of enrichment around the transcriptional start site. In addition to a common consensus 6mA site found in other eukaryotes, novel 6mA sites were found, indicating that 6mA could evolve new functions in land plants. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA positively correlates with the gene expression level in Col plants. Consistently, DNA affinity chromatography coupled with mass spectrometry reveals that histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, indicating that 6mA could serve as a potentially novel epigenetic mark in land plants.
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Project description:In mammalian cells, DNA methylation on the 5th position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N6-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, we identify a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylation of histone H3K4me2 and 6mA, and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data identify a novel DNA modification in C. elegans and raise the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes.
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