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

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

PROVIDER: PRJNA1036575 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26700800_1.fastq.gz	Fastqsanger.gz
	SRR26700800_2.fastq.gz	Fastqsanger.gz
	SRR26700801_1.fastq.gz	Fastqsanger.gz
	SRR26700801_2.fastq.gz	Fastqsanger.gz
	SRR26700790_1.fastq.gz	Fastqsanger.gz

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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.

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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.

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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.

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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.

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