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Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [ChIP-Seq]

ABSTRACT: Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [ChIP-Seq]

PROVIDER: PRJNA848923 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19645650.fastq.gz	Fastqsanger.gz
	SRR19645651.fastq.gz	Fastqsanger.gz
	SRR19645652.fastq.gz	Fastqsanger.gz
	SRR19645653.fastq.gz	Fastqsanger.gz

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Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process

Project description:Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process

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Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [RNA-Seq]

Project description:Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [RNA-Seq]

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Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [ChIP-Seq]

Project description:Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. Here we show that knockout of HDC1 enhances transcriptome re-programming prior to growth arrest of salt-treated seedlings and we identify two genes that mediate the effect of salt stress downstream of HDC1. HDC1 attenuates their transcriptional response via a dual mechanism involving H3K9/14 de-acetylation and H3K27 trimethylation. The latter, but not the former, was dependent on the linker histone H1, which interacts with HDC1 via the conserved RXT3 domain. However, a truncated RXT3-like version of HDC1 was not sufficient to recover H3K27me3 deposition in hdc1 suggesting that H1-aided recruitment H3K27 methylation machinery also requires the full-length HDC1-interacting deacetylases. The apparent paradox of repressive marks on stress-induced genes reveals an 'anti-panic' device that employs HDC1 as epigenetic moderator of stress responsiveness offering a leaver to tune stress sensitivity in plants. To identify potential direct targets of HDC1 we isolated nuclei from control and salt-treated HDC1c and hdc1-1 seedlings and performed chromatin immunoprecipitation (ChIP) with an antibody against acetylated lysines 9 and 14 in histone 3 (anti-H3K9K14Ac).

2024-03-27 | GSE206054 | GEO

Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [RNA-Seq]

Project description:Plants respond to environmental challenges via a network of signalling pathways. Early responses prevent damage if the stress persists but delay growth in fluctuating conditions. Optimizing these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously shown that Histone Deacetylation Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the sensitivity of Arabidopsis seedlings to salt and ABA, but the underlying mechanism remained elusive. Here we show that knockout of HDC1 enhances transcriptome re-programming prior to growth arrest of salt-treated seedlings and we identify two genes that mediate the effect of salt stress downstream of HDC1. HDC1 attenuates their transcriptional response via a dual mechanism involving H3K9/14 de-acetylation and H3K27 trimethylation. The latter, but not the former, was dependent on the linker histone H1, which interacts with HDC1 via the conserved RXT3 domain. However, a truncated RXT3-like version of HDC1 was not sufficient to recover H3K27me3 deposition in hdc1 suggesting that H1-aided recruitment H3K27 methylation machinery also requires the full-length HDC1-interacting deacetylases. The apparent paradox of repressive marks on stress-induced genes reveals an 'anti-panic' device that employs HDC1 as epigenetic moderator of stress responsiveness offering a leaver to tune stress sensitivity in plants. To identify genes underpinning salt tolerance in Arabidopsis thaliana and regulated by Histone Deacetylation Complex 1 (HDC1) we performed RNA-sequencing on HDC1 fully complemented line (HDC1c), hdc1-1 knock-out mutant (hdc1-1) and hdc1-1 mutant expressing the HDC1 domain RXT3 (RXT3). Seedlings were grown for 3 days on control plates and plates supplemented with 100 mM NaCl.

2024-03-27 | GSE205893 | GEO

Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process

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

2024-03-27 | GSE206055 | GEO

Effect of uniconazole on wt and pkl mutant germinating seeds

Project description:Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl).

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Dual-transcritome analysis of germinating Arabidopsis seeds in response to necrotrophic fungus Alternaria brassicicola

Project description:We analyzed dual-transcriptome changes in germinating Arabidopsis seeds at three development stages (3, 6 and 10 days after sowing) with or without Alternaria brassicicola. Differentailly expressed genes were identified from both seed and fungus.

2022-04-12 | GSE199977 | GEO

Identifying conserved and novel miRNAs in germinating seeds of Glycine max using deep sequencing

Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development. In soybean (Glycine max), an important edible oil crop, valuable lipids are synthesized and stored in the cotyledons during embryogenesis .This storage lipids are used as energy source of the emerging seeds, during the germination procces. Until now, there are no microRNAs related to lipid metabolism in soybean or any other plant. This work aims to describe the miRNAome of germinating seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus germinating seeds. A total of 183 familes were detected through a computational analysis of a large number of reads obtained from deep sequencing from two small RNA libraries of (i) pooled germintaing seeds stages and (ii) mature soybean seeds. We have found 39 new mirna precursors which produce 41 new mature forms. The present work also have identified isomiRNAs and mirnas offset (moRNAs). This work presents a comprehensive study of the miRNA transcriptome of soybean germinating seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in lipid consumption in development soybean seeds.

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