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Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [Bisulfite-seq]

ABSTRACT: Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [Bisulfite-seq]

PROVIDER: PRJNA811135 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18164482_1.fastq.gz	Fastqsanger.gz
	SRR18164482_2.fastq.gz	Fastqsanger.gz
	SRR18164483_1.fastq.gz	Fastqsanger.gz
	SRR18164483_2.fastq.gz	Fastqsanger.gz

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Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development

Project description:Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development

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Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [RNA-seq]

Project description:Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [RNA-seq]

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Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [RNA-seq]

Project description:We mutated PpDDM1 and the early land plant. Using BS-seq and RNA-seq, we here show that though DNA methylation is disrupted in all contexts development isn't and TE and gene differential expression are minute

2023-03-16 | GSE198691 | GEO

Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development [Bisulfite-seq]

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Mutating DDM1 in Physcomitrella patens disrupts DNA methylation with a minute effect on transposon regulation and development

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

2023-03-16 | GSE198693 | GEO

Knockout of DDM1 in Physcomitrium patens disrupts DNA methylation with a minute effect on transposon regulation and development.

Project description:The Snf2 chromatin remodeler, DECREASE IN DNA METHYLATION 1 (DDM1) facilitates DNA methylation. In flowering plants, DDM1 mediates methylation in heterochromatin, which is targeted primarily by MET1 and CMT methylases and is necessary for silencing transposons and for proper development. DNA methylation mechanisms evolved throughout plant evolution, whereas the role of DDM1 in early terrestrial plants remains elusive. Here, we studied the function of DDM1 in the moss, Physcomitrium (Physcomitrella) patens, which has robust DNA methylation that suppresses transposons and is mediated by a MET1, a CMT, and a DNMT3 methylases. To elucidate the role of DDM1 in P. patens, we have generated a knockout mutant and found DNA methylation to be strongly disrupted at any of its sequence contexts. Symmetric CG and CHG sequences were affected stronger than asymmetric CHH sites. Furthermore, despite their separate targeting mechanisms, CG (MET) and CHG (CMT) methylation were similarly depleted by about 75%. CHH (DNMT3) methylation was overall reduced by about 25%, with an evident hyper-methylation activity within lowly-methylated euchromatic transposon sequences. Despite the strong hypomethylation effect, only a minute number of transposons were transcriptionally activated in Ppddm1. Finally, Ppddm1 was found to develop normally throughout the plant life cycle. These results demonstrate that DNA methylation is strongly dependent on DDM1 in a non-flowering plant; that DDM1 is required for plant-DNMT3 (CHH) methylases, though to a lower extent than for MET1 and CMT enzymes; and that distinct and separate methylation pathways (e.g. MET1-CG and CMT-CHG), can be equally regulated by the chromatin and that DDM1 plays a role in it. Finally, our data suggest that the biological significance of DDM1 in terms of transposon regulation and plant development, is species dependent.

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RNA-seq for WT and ddm1(-/-) to evaluate transposon expression in ddm1 1st generation

Project description:Silencing of transposons by the chromatin remodeler DDM1 is mediated by the deposition of heterochromatic H2A variants. Transposon mobility and silencing participates in genome evolution but also threaten genome integrity. DECREASED DNA METHYLATION 1 (DDM1) belongs to a conserved family of chromatin remodelers that are required to silence transposons, yet the underlying molecular mechanism has remained unknown. Here we show that DDM1 binds the histone variant H2A.W through two conserved domains that are required to deposit H2A.W and maintain transposon silencing. The mechanism of transcriptional silencing described here is likely shared among chromatin remodelers of the DDM1 family and heterochromatic H2A variants that have evolved in mammals.

2021-02-10 | GSE150433 | GEO

RNA-seq for Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1

2021-02-10 | GSE150435 | GEO

DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis

Project description:Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. We also show that small RNA-directed DNA methylation (RdDM) is inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. DDM1 and RdDM independently mediate nearly all transposon methylation, which is catalyzed by the methyltransferases MET1 (CG), CMT3 (CHG), DRM2 (CHH) and CMT2 (CHH), and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that the Arabidopsis genome is defined by a heterochromatic continuum that governs the access of DNA methyltransferases and potentially all DNA binding proteins. Examination of DNA methylation, transcription and nucleosomes in Arabidopsis wild-type and/or ddm1, RdDM and DNA methylase mutants.

2013-04-17 | E-GEOD-41302 | biostudies-arrayexpress

DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis

2013-04-17 | GSE41302 | GEO