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The epigenetic Transcriptional factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene RNA silencing in Arabidopsis

ABSTRACT: The epigenetic Transcriptional factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene RNA silencing in Arabidopsis

PROVIDER: PRJNA719110 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14129513.fastq.gz	Fastqsanger.gz
	SRR14129514.fastq.gz	Fastqsanger.gz
	SRR14129515.fastq.gz	Fastqsanger.gz
	SRR14129516.fastq.gz	Fastqsanger.gz
	SRR14129517.fastq.gz	Fastqsanger.gz

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The epigenetic Transcriptional factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene RNA silencing in Arabidopsis

Project description:We examined global expression profiles of 5-day-old fve-8 seedlings compared to parental line (E5-4) using illumina sequencing

2021-04-07 | GSE171316 | GEO

FVE directly enriches to RdDM target loci.

Project description:Using ChIP-seq to study the deposition of FVE on the chromatin

2021-04-10 | GSE171808 | GEO

EXPORTIN 1A Prevents Transgene Silencing in Arabidopsis through Modulating the Nucleo-cytoplasmic Partitioning of HDA6

Project description:In eukaryotic cells, nucleo-cytoplasmic trafficking of macromolecules across the nuclear envelope is an essential process that ensures a rapid exchange of different cellular components, including proteins and RNAs, between the nucleus and cytoplasm. The significance of the nucleo-cytoplasmic trafficking of chromatin regulators in regulating DNA methylation and gene silencing is not well understood. Here, using a genetic screen, we identified XPO1A, one of the nuclear export receptors in Arabidopsis, as an anti-silencing factor that protects transgenes from transcriptional silencing. Loss-of-function of XPO1A leads to locus-specific DNA hypermethylation at transgene promoters and some endogenous loci. We found that XPO1A directly interacts with histone deacetylase HDA6 in vivo and the xpo1a mutation causes increased nuclear retention of HDA6 protein, resulting in reduced histone acetylation and enhanced transgene silencing. Our results revealed a new mechanism of epigenetic regulation through the modulation of XPO1A-dependent nucleo-cytoplasm partitioning of a chromatin regulator.

2019-01-12 | GSE119098 | GEO

FVE affects 24-nt siRNA accumulation downstream of RdDM pathway

Project description:Using siRNA-Seq to provide siRNA accumulation status in fve mutant.

2021-04-10 | GSE171813 | GEO

FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [Bisulfite-seq]

Project description:DNA methylation can be established by RNA-directed DNA methylation (RdDM) in plants. The association of RNA polymerase V (Pol V) with chromatin is a critical step for RdDM. While the SRA-domain-containing proteins SUVH2 and SUVH9 and the DDR complex are known to be required for the association of Pol V with chromatin, it is unknown whether the association of Pol V with chromatin requires other unidentified regulators. Here we found that SUVH9 is able to interact with a conserved histone-interaction protein, FVE, and a previously uncharacterized RRM domain-containing protein, which we named RRM1. We demonstrated that FVE facilitates the association of Pol V with chromatin and thus contributes to DNA methylation at a substantial subset of RdDM target loci, while RRM1 is only slightly involved in RdDM. FVE-dependent RdDM target loci are more abundant in gene-rich chromosome arms than FVE-independent RdDM target loci. FVE was previously shown to be a shared subunit of the RPD3-type histone deacetylase complex and the polycomb-type histone H3K27 trimethyltransferase complex, both of which are involved in transcriptional repression. This study reveals a previously uncharacterized role of FVE in RdDM and suggests that FVE may coordinate RdDM, histone deacetylation, and H3K27 trimethylation, thus ensuring transcriptional silencing of TEs in gene-rich chromosome arms to protect genes from harmful effects of potentially transcribed TEs.

2021-06-12 | GSE169178 | GEO

FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [RNA-seq]

2021-06-12 | GSE169174 | GEO

FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [ChIP-seq]

2021-06-12 | GSE169179 | GEO

FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [H3K27me3 ChIP-Seq].

2021-06-01 | GSE173630 | GEO

FVE regulates DNA methylation levels at a subset of RdDM loci.

Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in Col-0 WT, nrpd1-3, nrpe1-11 and fve-4.

2021-04-10 | GSE171805 | GEO

Endogenous small RNAs from Arabidopsis thaliana wild-type, dcl4 mutant and dcl4 mutant expressing nuclear or cytoplasmic DCL4

Project description:Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. A second, longer DCL4 transcript isoform encodes a nuclear-localization signal and its expression is repressed by DNA methylation. Consequently this isoform is induced when promoter methylation decreases due to infection with a bacterial pathogen or during silique development. Nuclear DCL4 produces unique populations of small RNAs, called DCL4NLS isoform-dependent siRNAs (disiRNAs), which function via a post-transcriptional silencing effector, but whose precursors are generated by the RdDM pathway. Arabidopsis cells can thus respond to genome methylation changes by modulating DCL4 localization, which in turn recruits PTGS factors to reinforce RNA silencing.

2016-11-14 | GSE74731 | GEO

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