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Non-CG methylation is more potent than CG methylation in moss genome regulation

ABSTRACT: Non-CG methylation is more potent than CG methylation in moss genome regulation

PROVIDER: PRJNA595741 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10694830.fastq.gz	Fastqsanger.gz
	SRR10694831.fastq.gz	Fastqsanger.gz
	SRR10694832.fastq.gz	Fastqsanger.gz
	SRR10694833.fastq.gz	Fastqsanger.gz
	SRR10694834.fastq.gz	Fastqsanger.gz

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Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens BS-Seq]

Project description:Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens BS-Seq]

| PRJNA595743 | ENA

Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens RNA-Seq]

Project description:Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens RNA-Seq]

| PRJNA595744 | ENA

Non-CG methylation is more potent than CG methylation in moss genome regulation [Athaliana RNA-Seq]

Project description:Non-CG methylation is more potent than CG methylation in moss genome regulation [Athaliana RNA-Seq]

| PRJNA595745 | ENA

Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens RNA-Seq]

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

Non-CG methylation is more potent than CG methylation in moss genome regulation [Athaliana RNA-Seq]

2020-12-30 | GSE142052 | GEO

Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens BS-Seq]

2020-12-30 | GSE142051 | GEO

Non-CG methylation is more potent than CG methylation in moss genome regulation

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-12-30 | GSE142054 | GEO

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

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

2014-03-13 | E-GEOD-46692 | biostudies-arrayexpress

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

2014-03-13 | GSE46692 | GEO

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Project description:DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 specifically binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines at sites that are also regulated by H3K9 dimethylation. By generating different combinations of non-CG methylation mutants, we reveal the contributions and redundancies between each methyltransferase in DNA methylation patterning and in regulating transposable elements (TEs) and protein-coding genes. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes.

2013-12-15 | GSE51304 | GEO

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