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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana Physcomitrium patens

PROVIDER: GSE142054 | GEO | 2020/12/30

REPOSITORIES: GEO

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

| PRJNA595741 | 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 BS-Seq]

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

| PRJNA595743 | ENA

DNA methylation mutants in <i>Physcomitrella patens</i> elucidate individual roles of CG and non-CG methylation in genome regulation.

Project description:Cytosine (DNA) methylation in plants regulates the expression of genes and transposons. While methylation in plant genomes occurs at CG, CHG, and CHH sequence contexts, the comparative roles of the individual methylation contexts remain elusive. Here, we present Physcomitrella patens as the second plant system, besides Arabidopsis thaliana, with viable mutants with an essentially complete loss of methylation in the CG and non-CG contexts. In contrast to A. thaliana, P. patens has more robust CHH methylation, similar CG and CHG methylation levels, and minimal cross-talk between CG and non-CG methylation, making it possible to study context-specific effects independently. Our data found CHH methylation to act in redundancy with symmetric methylation in silencing transposons and to regulate the expression of CG/CHG-depleted transposons. Specific elimination of CG methylation did not dysregulate transposons or genes. In contrast, exclusive removal of non-CG methylation massively up-regulated transposons and genes. In addition, comparing two exclusively but equally CG- or CHG-methylated genomes, we show that CHG methylation acts as a greater transcriptional regulator than CG methylation. These results disentangle the transcriptional roles of CG and non-CG, as well as symmetric and asymmetric methylation in a plant genome, and point to the crucial role of non-CG methylation in genome regulation.

| S-EPMC7777129 | biostudies-literature

Genetic effects on non-CG DNA methylation

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

2022-02-14 | GSE194406 | GEO

Transposon age and non-CG methylation.

Project description:Silencing of transposable elements (TEs) is established by small RNA-directed DNA methylation (RdDM). Maintenance of silencing is then based on a combination of RdDM and RNA-independent mechanisms involving DNA methyltransferase MET1 and chromodomain DNA methyltransferases (CMTs). Involvement of RdDM, according to this model should decrease with TE age but here we show a different pattern in tomato and Arabidopsis. In these species the CMTs silence long terminal repeat (LTR) transposons in the distal chromatin that are younger than those affected by RdDM. To account for these findings we propose that, after establishment of primary RdDM as in the original model, there is an RNA-independent maintenance phase involving CMTs followed by secondary RdDM. This progression of epigenetic silencing in the gene-rich distal chromatin is likely to influence the transcriptome either in cis or in trans depending on whether the mechanisms are RNA-dependent or -independent.

| S-EPMC7060349 | biostudies-literature

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