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Interplay between gene expression, histone modifications, and DNA methylation mediated by miR778 during beet cyst nematode parasitism of Arabidopsis [RNA-seq]

ABSTRACT: Interplay between gene expression, histone modifications, and DNA methylation mediated by miR778 during beet cyst nematode parasitism of Arabidopsis [RNA-seq]

PROVIDER: PRJNA727190 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14418068_1.fastq.gz	Fastqsanger.gz
	SRR14418068_2.fastq.gz	Fastqsanger.gz
	SRR14418069_1.fastq.gz	Fastqsanger.gz
	SRR14418069_2.fastq.gz	Fastqsanger.gz
	SRR14418070_1.fastq.gz	Fastqsanger.gz

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Project description:Purpose: The aim of this study is to investigate the role of H3K9 methylation in the development of syncytia induced by the beet cyst nematode (BCN, Heterodera schachtii). For this, ChIP-seq analysis was conducted in root tissues of Col-0 wild-type versus single suvh5 and suvh6 mutant plants and under BCN-infected and noninfected conditions. Methods: Methods: Col-0 wild-type and suvh5 and suvh6 mutant plants were grown and 10-day-old plants were inoculated with 100 second-stage juvenile (J2) H. schachtii at 10 days old. Five days post inoculation, root tissues were collected from infected and noninfected plants in triplicate. ChIP DNA was precipitated using the H3k9me2 antibody (Abcam) and prepared into libraries. Then, high throughput ChIP DNA sequencing was performed using the Illumina NovoSeq 6000. Raw reads were trimmed of adapter sequences and overrepresented reads. Then, high quality, paired-end reads were aligned to the Arabidopsis thaliana reference genome (TAIR10.28) using Bowtie2. Finally, histone peaks were called using MACS2 for the identification of genes associated with differentially dimethylated H3K9 in wild-type versus mutant roots under BCN-infected and noninfected conditions. Results and Conclusions: Under noninfected conditions, 511 and 143 H3K9me2 peaks were enriched in Col-0 compared to suvh5 and suvh6, respectively. The majority of these H3K9me2 peaks are located within TEs, which is consistent with previous findings that H3K9me2 corresponds to the repression of detrimental TEs. Our results suggest, however, that H3K9me2 adopts a new role in response to BCN. BCN-infected Col-0 had 791 H3K9me2 peaks compared to noninfected Col-0, 743 of which are located in the promoter or body of protein-coding genes. These peaks are associated with 1180 protein-coding genes. Similarly, suvh5 and suvh6 single mutants had 353 and 3106 H3K9me2 peaks compared to BCN-infected Col-0, respectively. The majority of these peaks are located in protein-coding genes and are associated with 558 and 4594 protein-coding genes, respectively. Interestingly, about 65% of peaks enriched in the BCN-infected wild type overlapped with peaks depleted in the suvh6 mutant, indicating that SUVH6 contributes to the majority of H3K9me2 during BCN parasitism.

Project description:Purpose: The aim of this study is to investigate the role of H3K9 methylation in the development of syncytia induced by the beet cyst nematode (BCN, Heterodera schachtii). For this, differential gene expression analysis was performed in root tissues of Col-0 wild-type and suvh5 and suvh6 single mutants under BCN-infected and noninfected conditions. Methods: Col-0 wild-type and suvh5 and suvh6 mutant plants were grown and 10-day-old plants were inoculated with 100 second-stage juvenile (J2) H. schachtii at 10 days old. Five days post inoculation, root tissues were collected from infected and noninfected plants in triplicate. Total RNA was extracted, mRNA libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovoSeq 6000. High quality, paired-end reads were then aligned to the Arabidopsis thaliana reference genome (TAIR10.28) using STAR and uniquely mapped reads were counted using HTSeq. Finally, differentially expressed genes (DEGs) between the mutant lines and wild-type plants under non-infected and infected conditions were identified using DESeq package. Results and conclusions: At least 20 million reads were uniquely mapped to the Arabidopsis reference genome with an average length of about 300 bp for paired-end reads. A total of 1057 and 3390 DEGs were identified for suvh5 and suvh6 versus Col-0, respectively, under noninfected conditions. Upon infection of BCN, Col-0 had 4566 DEGs compared to the noninfected wild type. BCN-infected single mutants suvh5 and suvh6 had 2487 and 846 DEGs compared to BCN-infected Col-0, respectively. Of these DEGs, 1277 and 592 or about 51% and 70% are also differentially expressed in BCN-infected Col compared to noninfected Col-0, respectively, and 324 of the 1277 and 592 DEGs are common to BCN-infected suvh5 and suvh6 compared to the control. DEGs common to BCN-infected Col-0 and/or suvh5, and suvh6 are involved in stress and defense responses, primary and secondary metabolism, signal transduction, cell wall organization and other cellular processes. This suggests that SUVH5 and SUVH6 play a major role in transcriptome reprogramming to facilitate cellular, molecular, and metabolic processes involved in the compatible plant-nematode interaction.

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Interplay between gene expression, histone modifications, and DNA methylation mediated by miR778 during beet cyst nematode parasitism of Arabidopsis [RNA-seq]

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