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Methylome dynamic upon proteasome inhibition by the pseudomonas virulence factor Syringolin A

ABSTRACT: Methylome dynamic upon proteasome inhibition by the pseudomonas virulence factor Syringolin A

PROVIDER: PRJNA729499 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14513412_1.fastq.gz	Fastqsanger.gz
	SRR14513412_2.fastq.gz	Fastqsanger.gz
	SRR14513413_1.fastq.gz	Fastqsanger.gz
	SRR14513413_2.fastq.gz	Fastqsanger.gz
	SRR14513414_1.fastq.gz	Fastqsanger.gz

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Methylome dynamic upon proteasome inhibition by the pseudomonas virulence factor Syringolin A

Project description:DNA methylation is an important epigenetic mark required for proper gene expression and silencing of transposable elements. DNA methylation patterns can be modified by environmental factors such as pathogen infection, where modification of DNA methylation can be associated with plant resistance. To counter the plant defense pathways, pathogens produce effectors molecule, several of which act as proteasome inhibitors. Here we investigated the effect of proteasome inhibition by the bacterial virulence factor Syringolin A on genome-wide DNA methylation. We show that Syringolin A treatment results in an increase of DNA methylation at centromeric and pericentromeric regions of Arabidopsis chromosomes. We identify several CHH DMRs that are enriched in the proximity of transcriptional start sites. Syringolin A treatment does not result in significant changes in small RNA composition. However, significant changes in genome transcriptional activity can be observed, including a strong upregulation of resistance genes that are located on chromosomal arms. We hypothesize that DNA methylation changes could be linked to the upregulation of some atypical members of the de novo DNA methylation pathway: AGO3, AGO9 and DRM1. Our data suggests that modification of genome-wide DNA methylation resulting from an inhibition of the proteasome by bacterial effectors could be part of a epi-genomic arms race against pathogens.

2023-07-04 | GSE174350 | GEO

Reversal of Aberrant Cancer Methylome and Transcriptome upon Direct Reprogramming of Lung Cancer Cells.

Project description:This SuperSeries is composed of the following subset Series: GSE35911: Reversal of Aberrant Cancer Methylome and Transcriptome upon Direct Reprogramming of Lung Cancer Cells [Expression] GSE35912: Reversal of Aberrant Cancer Methylome and Transcriptome upon Direct Reprogramming of Lung Cancer Cells [Methylation] Refer to individual Series

2012-08-27 | E-GEOD-35913 | biostudies-arrayexpress

Dynamic behavior of the epigenetic machinery upon thermal stress

Project description:Dynamic behavior of the epigenetic machinery upon thermal stress

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The 26S proteasome substrates and the dynamics of nuclear proteome upon DNA damage

Project description:Upon DNA damage, numerous proteins are targeted for ubiquitin-dependent proteasomal degradation. We show that phosphorylation of Rpn10/PSMD4 (ubiquitin receptor of the proteasome) at Ser266, is required for DNA repair. Here, we performed TurboID proximity labeling for capturing the proteasome substrates under DNA damage. Numerous proteins which involve in DNA damage response, chromosome reorganization cell cycle and histone modification were identified as the potential pronuteasome substrates. We find that DNA damage reduced the overall affinity between substrates and wild-type Rpn10 compared to Rpn10-Ser266 mutant cells. Combining TMT quantitative proteomic studies, we observed the dynamics of more than 2,000 nuclear proteins upon DNA damage and time course release. Most proteins were accumulated in wild-type cells in the time course release, while the Rpn10-Ser266 mutant cells show almost no changes in protein level. These findings reveal an inherent self-limiting mechanism of the proteasome that, by controlling substrate recognition through Rpn10 phosphorylation, fine-tunes protein degradation for optimal responses under stress.

2023-11-28 | PXD047298 |

Dynamic changes in liver 5-hydroxymethylcytosine profiles upon non-genotoxic carcinogen exposure [Replicated control vs. pb treated study]

Project description:Dynamic changes in the mouse liver DNA methylome associated with short (1 day) and prolonged (7, 28 and 91 days) exposure to the rodent liver non-genotoxic carcinogen (NGC), phenobarbital (PB). Full expression dataset (all time points: 1, 7, 28, 91 days) Replicated control vs. pb treated study

2013-03-25 | E-GEOD-45465 | biostudies-arrayexpress

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition

Project description:Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition

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Genome-wide mapping of NRF1 (NFE2L1) binding in HCT116 cells upon proteasome inhibition.

Project description:Genome-wide mapping of NRF1 (NFE2L1) binding in HCT116 cells upon proteasome inhibition.

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Dissecting the Dynamic Changes of Methylome and Transcriptome During Rice Transformation

Project description:Dissecting the Dynamic Changes of Methylome and Transcriptome During Rice Transformation

| PRJNA837100 | ENA

Dynamic changes in liver 5-hydroxymethylcytosine profiles upon non-genotoxic carcinogen exposure [Replicated control vs. pb treated study]

2013-03-25 | GSE45465 | GEO

Genome-wide mapping of NRF1 (NFE2L1) binding in HCT116 cells upon proteasome inhibition.

Project description:The maintenance of protein homeostasis is an essential characteristic of life. Transcription factor NRF1 (NFE2L1) has been reported to be activated by proteasome dysfunction, although the genome-wide target genes are poorly understood. Using ChIP-seq analysis, we found a potential association between NRF1 and autophagy. Our findings highlight the new activation mechanism of autophagy through gene regulation under proteasome dysfunction.

2023-03-19 | GSE227357 | GEO

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