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Coprinopsis cinerea

ABSTRACT: Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [CMS-seq]

PROVIDER: PRJNA203154 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR851215.fastq.gz	Fastqsanger.gz
	SRR851216.fastq.gz	Fastqsanger.gz
	SRR851217.fastq.gz	Fastqsanger.gz
	SRR851218.fastq.gz	Fastqsanger.gz
	SRR851219.fastq.gz	Fastqsanger.gz

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Coprinopsis cinerea

Project description:Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [RNA-seq]

| PRJNA253741 | ENA

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea

Project description:Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea

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Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [RNA-seq]

Project description:TET/JBP enzymes oxidize 5-methylpyrimidines in DNA. In mammals, the oxidized methylcytosines (oxi-mC) function as epigenetic marks and likely intermediates in DNA demethylation. Here we present a novel diglucosylation-based method to simultaneously map 5hmC, 5fC and 5caC at near base-pair resolution, and verify the results using independent methods. We have used the method to map the distribution of oxi-mC across the genome of Coprinopsis cinerea, a basidiomycete that encodes 47 TET/JBP paralogs in a new class of DNA transposons. Like 5-methylcytosine (5mC) residues from which they are derived, oxi-mC modifications are enriched at centromeres, TET/JBP transposons, and multicopy paralogous genes that are not expressed, but rarely mark genes whose expression changes between two developmental stages. Our study provides evidence for the emergence of an epigenetic regulatory system through recruitment of selfish elements in a eukaryotic lineage, and describes a method to map all three different species of oxi-mC simultaneously.

2014-12-02 | GSE58865 | GEO

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [CMS-seq]

2014-12-02 | GSE46963 | GEO

Coprinopsis cinerea

Project description:PacBio RS sequencing of oxidized methylcytocines in Coprinopsis cinerea

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5mC oxidation products in the nucleic acids of the Basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea

Project description:We analyzed oxidized 5-methylcytosine derivatives 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in nucleic acids of multicellular fungi Laccaria bicolor and Coprinopsis cinerea which have been used as models to study DNA methylation, developmental processes and symbiotic interactions. All three cytosine derivatives were detected in the genomes of both fungi, and importantly, we discovered 5carC in the RNA fractions, potentially including large non-coding, messenger RNAs and small RNA molecules, indicating gene regulatory functions of 5carC.

2022-01-16 | GSE185550 | GEO

omparison of gene expression during meiosis between wild-type and deficient strains of Coprinopsis cinerea

Project description:This SuperSeries is composed of the following subset Series: GSE37942: Comparison of gene expression during meiosis between wild-type and rad50-deficient strains of Coprinopsis cinerea GSE37943: Comparison of gene expression during meiosis between wild-type and msh5-deficient strains of Coprinopsis cinerea Refer to individual Series

2012-05-14 | E-GEOD-37968 | biostudies-arrayexpress

The meiotic transcriptome of the basidomycete fungus Coprinopsis cinerea (Coprinus cinereus)

Project description:Coprinopsis cinerea exhibits synchronised meiosis in the gill tissue of the fungus, which is 75% meiotic. The mushroom develops from a dikaryon, which contains two separate nuclei. These nucleifuse in the basidia (karyogamy). After karyogamy, the nuclei enter an extended meiotic prophase, in which pahcytene occurs at 6 hours post karyogamy (K+6). The tetrads produced by the second meiotic division are present 12 hours after karyogamy (K+12). To examine a comprehensive timecourse of meiosis in this organism, we took samples over a 15-hour period, 3 hours apart: K-3, K, K+3, K+6, K+9, K+12. Keywords: time course

2010-02-01 | GSE13731 | GEO

Coprinopsis cinerea transcriptome in response to hyphal damage, nematode predation or bacterial co-cultivation

Project description:We have recently shown that the coprophilous model mushroom Coprinopsis cinerea transcribes a broad array of genes encoding defense proteins in the vegetative mycelium and fruiting bodies that target bacterial competitors and animal predators challenging the respective tissues of this fungus. In addition, we have demonstrated in previous work that two nematotoxic defense proteins from Coprinopsis, CGL1 and CGL2, were induced in vegetative mycelium challenged with the predatory nematode Aphelenchus avenae; however, the specificity and broadness of this response remained unclear. In order to resolve these issues, we sequenced the poly(A)-positive transcriptome of vegetative mycelium of C. cinerea confronted with nematode predation, hyphal mechanical damage or bacterial co-culture.

2015-09-01 | E-MTAB-2763 | biostudies-arrayexpress

Coprinopsis cinerea

Project description:Coprinopsis cinerea Raw sequence reads

| PRJNA682885 | ENA