DNA N6-adenine methylation in 3-week-old Arabidopsis thaliana [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA418775 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6298221_1.fastq.gz | Fastqsanger.gz | |||
| SRR6298221_2.fastq.gz | Fastqsanger.gz | |||
| SRR6298222_1.fastq.gz | Fastqsanger.gz | |||
| SRR6298222_2.fastq.gz | Fastqsanger.gz | |||
| SRR6298223_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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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.
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Project description:DNA N6-adenine methylation in Arabidopsis thaliana
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Project description:DNA N6-adenine methylation in Arabidopsis thaliana [SMRT-seq]
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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: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.
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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 | GSE81596 | 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:Elucidation of DNA Methylation on N6-Adenine with Deep Learning
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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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Project description:Comparison of TopHat alignments and assessment of spurious splice junctions for 32nt and 76nt read lengths. Total RNA from 2-week-old Arabidopsis thaliana (ecotype Columbia) seedlings grown on MS plates was isolated using RNeasy Plant Mini Kit from Qiagen. To remove any contaminating DNA, RNA was treated with DNAse. Isolation of poly (A) mRNA and preparation of cDNA library were carried out using the Illumina TrueSeq RNA kit. Sequencing (72 cycle) was done on Illumina Genome Analyzer II.
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