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Transcriptome and epigenome data analysis to reveal the key role of KAKU4 during leaf senescence in Arabidopsis

ABSTRACT: Transcriptome and epigenome data analysis to reveal the key role of KAKU4 during leaf senescence in Arabidopsis

PROVIDER: PRJNA1053328 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27228273.fastq.gz	Fastqsanger.gz
	SRR27228274.fastq.gz	Fastqsanger.gz
	SRR27228275_1.fastq.gz	Fastqsanger.gz
	SRR27228275_2.fastq.gz	Fastqsanger.gz
	SRR27228276_1.fastq.gz	Fastqsanger.gz

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Transcriptome and epigenome data analysis to reveal the key role of KAKU4 during leaf senescence in Arabidopsis

Project description:We conducted the combination analysis of transcriptomic and epigenomic data between kaku4-2 mutant and WT suggested that KAKU4 may inhibit the expression of a series of genes related to hormone signals and H2O2 metabolism by affecting the deposition of H3K27me3, thereby suppressing leaf senescence.

2024-02-09 | GSE250299 | GEO

Genome-wide transcriptome and epigenome data analysis of kaku4-2 mutant and WT plants

Project description:We conducted ChIP-seq technology to generate epigenomic profiles of H3K4me3, H3K27me3 and H3K9me2 in Arabidopsis leaves for the mutant (kaku4-2) and wild-type (WT) plants. The results showed that knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least effect on H3K4me3, leading to significant change of chromatin states in Arabidopsis genome. KAKU4 may affect the switch between active and repressive chromatin states, especially knockdown of KAKU4 caused the transition between H3K9me2 and H3K27me3 in some specific PLAD regions. The combination analysis of epigenomic and transcriptomic data between kaku4-2 mutant and WT suggested that KAKU4 may regulate some key biological processes, especially programmed cell death and hormone signaling pathways.

2024-02-29 | GSE247174 | GEO

Genome-wide KAKU4-eYFP ChIP-seq of Arabidopsis thaliana kaku4 complemented and untagged control plants at seedling (10 days) and 120-day rosette stages

Project description:Chromatin immunoprecipitation sequencing (ChIP-seq) was used to map the genome-wide binding profile of the inner nuclear envelope protein KAKU4 in Arabidopsis thaliana. A functional ProKAKU4:KAKU4-eYFP transgene (Goto et al., Plant Cell 2014), which complements the kaku4-3 mutant, and an untagged kaku4 (SALK_076754) control line were analysed. Young samples consisted of 10-day-old seedlings (n = 3 biological replicates per genotype, pooling ~12 seedlings per replicate). Old samples consisted of 120-day short-day rosettes, where senescence leaves from 3–4 plants were pooled per replicate (n = 3 replicates). Together enabling comparison of KAKU4 occupancy between juvenile and long-term aged tissues.

2026-08-08 | E-MTAB-16266 | biostudies-arrayexpress

KAKU4 regulates leaf senescence through modulation of H3K27me3 deposition in the Arabidopsis genome.

Project description: Not available

| S-EPMC10919013 | biostudies-literature

Genome-wide transcriptome and epigenome data analysis of kaku4-2 mutant and WT plants

Project description:Genome-wide transcriptome and epigenome data analysis of kaku4-2 mutant and WT plants

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Whole-genome methylome sequencing (EM-seq) of Arabidopsis thaliana Col-0, nuclear-envelope mutants crwn1–4, crwn1 crwn4 and kaku4 at 12 and 150 days after sowing under short-day conditions

Project description:Enzymatic methyl-seq (EM-seq) was used to profile whole-genome cytosine methylation in Arabidopsis thaliana wild type and nuclear-envelope mutants that display premature aging phenotypes. All lines are in the Col-0 background and include wild-type Col-0, single mutants in crwn1, crwn2, crwn3, crwn4 and kaku4, the crwn1 crwn4 double mutant, and a second-generation kaku4 line (kaku4-G2). For late-age samples, rosette tissue was harvested from soil-grown plants under short-day conditions (8 h light / 16 h dark) at 150 days after sowing, when nuclear-envelope mutants show strong rosette senescence, meristem failure and reduced lifespan. For young reference samples, whole seedlings of Col-0 (wildtype) and kaku4-G2 were collected at 12 days after sowing. For each genotype and age, pooled material from multiple plants was used to obtain sufficient genomic DNA. Genomic DNA was extracted from each pooled sample and converted using the NEBNext Enzymatic Methyl-seq (EM-seq) protocol, followed by Illumina library preparation and paired-end high-throughput sequencing. This dataset is used to (i) quantify genome-wide CG, CHG and CHH methylation in wild type and nuclear-envelope mutants, (ii) compare age-dependent methylation drift between 12-day seedlings and 150-day short-day rosettes, and (iii) identify chromatin-state- and transposable-element-specific methylation changes associated with nuclear-envelope dysfunction and premature aging in Arabidopsis.

2026-07-22 | E-MTAB-16263 | biostudies-arrayexpress

Foxp3 is a key downstream regulator of p53-mediated cellular senescence

Project description:The downstream events and target genes of p53 in senescence responses are not fully understood. Here, we report a novel function of the forkhead transcription factor Foxp3, a key player in mediating T cell inhibitory function, in p53-mediated cellular senescence. Overexpression of Foxp3 in mouse embryonic fibroblasts (MEFs) accelerates senescence, whereas Foxp3 knockdown leads to escape from p53-mediated senescence in p53-expressing MEFs. Consistently, Foxp3 expression resulted in the induction of senescence in epithelial cancer cells, including MCF7 and HCT116. Foxp3 overexpression also increased the intracellular levels of reactive oxygen species (ROS). The ROS inhibitor N-acetyl-L-cysteine rescued Foxp3 expression-induced senescence. Furthermore, the elevated ROS levels that accompanied Foxp3 overexpression were paralleled by an increase in p21 expression. Knockdown of p21 in Foxp3-expressing MEFs abrogated the Foxp3-dependent increase in ROS levels, indicating that Foxp3 acts through p21 induction and subsequent ROS elevation to trigger senescence. Collectively, these results suggest that Foxp3 is a downstream target of p53 that is sufficient to induce p21 expression and ROS production and is necessary for p53-mediated senescence. control and treated samples (human), young passage (p3) or old passage (p7) samples (mouse)

2015-08-13 | E-GEOD-71980 | biostudies-arrayexpress

Barely leaf dark-induced senescence

Project description:Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments. Time-course experiment, two-color, common reference design. All of the data were obtained from material collected in three independent, time-separated leaf senescing experiments (biological replicates). In each replicate, samples from senescing leaves (3 Days, 7 Days, 10 Days) were compared to samples collected before the senescence induction (Day 0). 3 biological replicates.Cy5-labeled samples of interest (Day 0, Day 3, Day 7 and Day 10 from each biological replicate) were each hybridized against a Cy3-labeled common reference (RNA pool of all samples) on a total of 12 microarrays.

2014-10-22 | E-GEOD-62539 | biostudies-arrayexpress

Barley leaf dark-induced senescence

2014-10-22 | GSE62539 | GEO

Dynamic antagonism between key repressive pathways maintains the placental epigenome

Project description:Dynamic antagonism between key repressive pathways maintains the placental epigenome

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