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Profiling DNA methylation in nematodes

ABSTRACT: DNA methylation in basal nematodes analysed by bisulfite sequencing

ORGANISM(S): Romanomermis culicivorax Trichuris muris Trichinella spiralis Plectus sambesii

PROVIDER: GSE104339 | GEO | 2018/01/01

SECONDARY ACCESSION(S): PRJNA412389

REPOSITORIES: GEO

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Profiling DNA methylation in nematodes

Project description:Profiling DNA methylation in nematodes

| PRJNA412389 | ENA

DNA hypomethylation confers enhanced immunity against parasitic nematodes in plants

Project description:Background: Epigenetic processes play an important role in the plant response to adverse environmental conditions. A role for DNA hypomethylation has recently been suggested in the pathogenic interaction between bacteria and plants, yet it remains unclear whether this phenomenon reflects a conserved and general plant immunity response. We therefore investigated the role of DNA methylation in the plant defence against damaging parasitic nematodes. Methods and results: Treatment of roots of rice (monocot plant) and tomato (dicot plant) by a nematode-associated molecular pattern (NAMP) from different parasitic nematodes revealed global DNA hypomethylation using ELISA based quantification, suggesting conservation among plants. Focusing on root-knot induced gall tissue in rice, the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon 5-Azacitidine treatment. Whole genome bisulfite sequencing revealed that hypomethylation was massively present in the CHH context, while absent for CpG or CHG nucleotide contexts. CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point, but rather showed a delayed effect on transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway (RdDM) and DDM1, which are known to be steering DNA methylation in CHH context. Conclusions: We demonstrated that DNA hypomethylation confers enhanced defence in rice towards root-parasitic nematodes and is likely to be part of the basal NAMP-triggered immunity response in plants.

2020-07-07 | GSE130064 | GEO

Clinical Study of Pan-cancer DNA Methylation Test in Plasma

Project description:We intend to establish an efficient method for plasma cfDNA extraction and Bisulfite transformation to facilitate the detection of DNA methylation status using multiplex fluorescence PCR. Meanwhile, we expect to identify several plasma methylation markers that can be highly sensitive for multi-cancer detection. Finally, we will provide a pan-cancer blood test that is easy to operate, low cost, accurate and easy to promote.

| 5068 | ecrin-mdr-crc

MinION DNA barcoding of nematodes

Project description:DNA barcoding of nematodes using the MinION

| PRJEB37489 | ENA

Profiling the DNA methylation pattern in naïve induced Pluripotent Stem cells and somatic cells

Project description:We analysed by Reduced Representation Bisulfite Sequencing (RRBS) the genome methylation pattern in human fibroblast and in naïve induced pluripoent stem cells (niPSCs)

2018-12-31 | GSE110366 | GEO

Genome-wide, High Resolution DNA Methylation Profiling Using Bisulfite-Mediated Cytosine Conversion

Project description:We developed a genome-wide DNA methylation profiling technology that determines methylation patterns using small amounts of starting material. This process involves a novel amplification step for DNA subjected to bisulfite-mediated cytosine conversion and generates highly reproducible datasets with low technical variation. The technology, named BiMP (for Bisulfite Methylation Profiling), is more cost-effective than mC immunoprecipitation techniques (mCIP) and can be applied to as little as 100 ng of Arabidopsis DNA. It is anticipated that this technology can be applied to mammalian genomes and may allow methylation profiling of a small number of physiologically uniform cells. Keywords: bisulfite DNA methylation profiling, Arabidopsis, methylation polymorphisms, met1-3,

2007-11-30 | GSE9051 | GEO

Nematodes

Project description:Nematodes Metagenome

| PRJNA836018 | ENA

Genome-wide profiling of DNA methylation patterns in iAs-transformed cells

Project description:To examine the global impact of iAs on DNA methylation patterns. Genomic DNA was Bisulfite converted and analyzed using Mini methly-seq.

2017-03-08 | GSE85012 | GEO

DNA methylation Profiling in Autoimmune encephalitis (AE): DNA methylation profile in healthy control (HC) sujects and acute-phase AE subjects

Project description:DNA methylation analysis of DNA samples from total WBC collection The DNA samples from each subject was first subject to bisulfite conversion, followed by sample preparation and microarray experiment.

2019-10-25 | GSE132866 | GEO

Genome-wide DNA methylation level analysis in plants overexpressing METS1

Project description:We report here with this study the genome-wide DNA methylation level analysis at single-nucleotide resolution by Next Gen bisulfite-sequencing using the Methyl-MaxiSeq platform from Zymo Research Services (Irvine, CA) in plants overexpressing the gene 5-Methyltetrahydropteroyltriglutamate Homocysteine Methyltransferase1 (METS1) comparatively to Col-0 plants both basal conditions and following Pseudomonas syringae DC3000 infection.

2019-05-14 | GSE128768 | GEO

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