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Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [small RNA-seq]

ABSTRACT: Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [small RNA-seq]

PROVIDER: PRJNA1144134 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30126603.fastq.gz	Fastqsanger.gz
	SRR30126604.fastq.gz	Fastqsanger.gz
	SRR30126605.fastq.gz	Fastqsanger.gz
	SRR30126606.fastq.gz	Fastqsanger.gz
	SRR30126607.fastq.gz	Fastqsanger.gz

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Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [WGBS]

Project description:Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [WGBS]

| PRJNA1144133 | ENA

Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [RNA-seq]

Project description:Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [RNA-seq]

| PRJNA1144135 | ENA

Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [WGBS]

Project description:Tomato is a major global crop however its production is limited by Botrytis cinerea. Due to the toxicity of post-harvest pesticide application, alternative control methods such as priming are being investigated. Plants were treated with β-aminobutyric (BABA) at two developmental stages and resistance against B. cinerea was tested in fruit tissue and in progenies. DNA methylation and RNA sequencing were conducted to characterise the (epi)genetic changes associated with long-lasting resistance. Grafting experiments were done to assess the systemic nature of this signal, which was further characterised by small RNA (sRNA) sequencing of scions. Only BABA-treated seedlings displayed induced resistance (IR). DNA methylation analysis revealed seedling-specific changes, which occurred in the context of lower basal methylation. BABA-IR was found to be transmissible from primed rootstock to grafted unprimed scions. In these scions, we identified a subset of mobile 24 nt sRNAs associated with primed genes to infection in fruit. Our results demonstrate the functional association of a systemic signal with long lasting IR and priming. Through integrated omics approaches we have identified markers of long-lasting priming in tomato fruit which could also serve as targets for durable resistance in other crops.

2024-11-17 | GSE273942 | GEO

Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [RNA-seq]

2024-11-17 | GSE273944 | GEO

Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [small RNA-seq]

2024-11-17 | GSE273943 | GEO

Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation

Project description:Exposure of plants to stress conditions or to certain chemical elicitors can establish a primed state, whereby responses to future stress encounters are enhanced. Stress priming can be long-lasting and likely involves epigenetic regulation of stress-responsive gene expression. However, the molecular events underlying priming are not well understood. Here, we characterise epigenetic changes in tomato plants primed for pathogen resistance by treatment with β-aminobutyric acid (BABA). We used whole genome bisulphite sequencing to construct tomato methylomes from control plants and plants treated with BABA at the seedling stage, and a parallel transcriptome analysis to identify genes primed for the response to inoculation by the fungal pathogen, Botrytis cinerea. Genomes of plants treated with BABA showed a significant reduction in global cytosine methylation, especially in CHH sequence contexts. Analysis of differentially methylated regions (DMRs) revealed that CHH DMRs were almost exclusively hypomethylated and were enriched in gene promoters and in DNA transposons located in the chromosome arms. Although there was some enrichment of stress response-related gene ontology terms in genes overlapping CHH DMRs, there was no significant enrichment of DMRs amongst a set of 747 primed defence genes, and nor was the pattern of methylation in these genes altered by BABA treatment. Hence, we conclude that whilst BABA treatment of tomato seedlings results in characteristic changes in genome-wide DNA methylation, CHH hypomethylation does not appear to directly target genes showing primed responses to pathogen infection. Instead, methylation may confer priming via in-trans regulation, acting at a distance from defence genes, and/or by targeting a smaller group of regulatory genes controlling stress responses.

2022-04-05 | GSE190780 | GEO

Type-I interferon priming signal balances anti-bacterial and anti-tumor trained immunity in alveolar macrophages [RNA-seq]

Project description:Tissue-resident macrophages may be trained to confer enhanced response to heterologous re-stimulation, and thus foster versatile trained immunity (TI) against both infections and tumors. However, key priming signals that contribute to such functional versatility in trained macrophages remain not fully understood. Here we show that influenza A virus (IAV) infection in mice induces lasting transcriptional imprints of acute type-I interferon (IFN-I) signaling in lung-resident alveolar macrophages (AMs) that confer balanced anti-bacterial and anti-tumor TI responses. In both IAV-infected mice and an ex vivo cytokine-mediated training system, IFN-I signaling is found to be critical to developing anti-tumor TI functions, although it limits anti-bacterial TI functions in AMs. Moreover, human AMs carrying transcriptional imprints of IFN-I signaling are associated with anti-tumor immunity and immune activation in lung cancer tissues. Our findings highlight IFN-I as a key priming signal required to developing versatile TI functions in AMs with balanced anti-bacterial and anti-tumor potential.

2025-05-07 | GSE295483 | GEO

Type-I interferon priming signal balances anti-bacterial and anti-tumor trained immunity in alveolar macrophages [ATAC-seq]

2025-05-07 | GSE295482 | GEO

Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation.

Project description:Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation.

| PRJNA788467 | ENA

Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation

Project description:Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation

| PRJNA788469 | ENA