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Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (BS-seq)

ABSTRACT: Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (BS-seq)

PROVIDER: PRJNA1219519 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32237715_1.fastq.gz	Fastqsanger.gz
	SRR32237715_2.fastq.gz	Fastqsanger.gz
	SRR32237716_1.fastq.gz	Fastqsanger.gz
	SRR32237716_2.fastq.gz	Fastqsanger.gz
	SRR32237717_1.fastq.gz	Fastqsanger.gz

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Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (BS-seq)

Project description:The tight coordination of sulfur metabolism and growth regulation is predicated upon nutrient availability. Central to this balancing act is the utilization of cysteine (Cys) for the formation of methionine (Met) and S-adenosylmethionine (SAM). Plants that are severely deficient in regenerating Met due to reduced methylthioadenosine (MTA) nucleosidase activity experience numerous developmental abnormalities. Here we assess the developmental, metabolic, and regulatory effects associated with decreased MTA recycling. We show that MTA over-accumulation predominantly occurs in reproductive tissues and leads to reduced levels of Cys, Met, and SAM, as well as elevated S-adenosylhomocysteine. These disruptions of primary sulfur utilization also lead to the misregulation of energy metabolism and altered cell cycle progression. RNA-seq experiments show a general down-regulation of many developmental and reproductive genes. Targeted metabolite analyses demonstrate clear impacts on the methyl index which are reflected in the results of bisulfite-sequencing experiments including global alterations in CG gene-body methylation levels and decreases of CHG and CHH methylation in transposable elements. Our findings demonstrate the broad impacts of MTA metabolism on plant development, sulfur utilization and the maintenance of the methyl index.

2025-03-16 | GSE288808 | GEO

Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis

Project description:Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis

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Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (RNA-seq)

Project description:Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (RNA-seq)

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Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (RNA-seq)

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Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis

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

2025-03-16 | GSE288809 | GEO

Bacillus sp. BS strain:BS

Project description:Bacillus sp. BS strain:BS Genome sequencing

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In Vitro Transcription Recycling Assay Identifies PAF1 as a Driver of RNA Pol II Recycling

Project description:RNA Polymerase II transcriptional recycling is an underappreciated mechanism for which the required factors and contributions to overall gene expression levels are poorly understood. We describe an in vitro methodology facilitating unbiased identification of novel RNA Pol II transcriptional recycling factors and quantitative measurement of transcriptional output from recycled transcriptional components. Proof-of-principle experiments identified PAF1 complex components among recycling factors and detected defective transcriptional output from RNA Pol II recycling following PAF1 depletion. Dynamic ChIP-seq confirmed in vivo PAF1 complex cycling through gene bodies with RNA Pol II and recycling back to the transcription start sites, while PAF1 silencing triggered defective RNA Pol II recycling. Prostate tumors exhibited enhanced transcriptional recycling, which was attenuated by antibody-based PAF1 depletion. These findings identify RNA Pol II recycling as a potential target in cancer and demonstrate the assay’s applicability to characterize RNA Pol II recycling in cells and tissues from other disease states.

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Project description:BS sufu Raw sequence reads

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Project description:Lysinibacillus sphaericus strain:BS-pBtoxis | isolate:BS-pBtoxis Genome sequencing

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Chromatin state for BS and M cells

Project description:We report the ChIP-seq of several histone modification markers for BS cells and H3K36me3 ChIP-seq for M cells, we found that BS-specific gene module trend to be regulated by histone acetylation.

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