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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE169180 | GEO | 2021/06/01

REPOSITORIES: GEO

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

2021-06-12 | GSE169178 | 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 promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin

Project description:FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin

| PRJNA715485 | ENA

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

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

| PRJNA715474 | ENA

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

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

| PRJNA715486 | ENA

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

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

| PRJNA715488 | ENA

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

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

| PRJNA726434 | ENA

MSI4/FVE is required for accumulation of 24-nt siRNAs and DNA methylation at a subset of target regions of RNA-directed DNA methylation.

Project description:DNA methylation is an important epigenetic mark. In plants, de novo DNA methylation occurs mainly through the RNA-directed DNA methylation (RdDM) pathway. Researchers have previously inferred that a flowering regulator, MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)/FVE, is involved in non-CG methylation at several RdDM targets, suggesting a role of FVE in RdDM. However, whether and how FVE affects RdDM genome-wide is not known. Here, we report that FVE is required for DNA methylation at thousands of RdDM target regions. In addition, dysfunction of FVE significantly reduces 24-nucleotide siRNA accumulation that is dependent on factors downstream in the RdDM pathway. By using chromatin immunoprecipitation and sequencing (ChIP-seq), we show that FVE directly binds to FVE-dependent 24-nucleotide siRNA cluster regions. Our results also indicate that FVE may function in RdDM by physically interacting with RDM15, a downstream factor in the RdDM pathway. Our study has therefore revealed that FVE, by associating with RDM15, directly regulates DNA methylation and siRNA accumulation at a subset of RdDM targets.

| S-EPMC9292519 | biostudies-literature

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