Similar Datasets
Project description:FVE directly enriches to RdDM target loci.
| PRJNA720941 | ENA
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
Project description:Using siRNA-Seq to provide siRNA accumulation status in fve mutant.
2021-04-10 | GSE171813 | GEO
Project description:FVE regulates DNA methylation levels at a subset of RdDM loci.
| PRJNA720939 | ENA
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 | GSE169179 | GEO
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
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
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
2021-06-01 | GSE173630 | GEO
Project description:Many plants, including Arabidopsis thaliana, respond to elevated ambient temperatures by altering their growth through a process known as thermomorphogenesis. This response involves the depletion of the repressive histone variant H2A.Z from the gene bodies of PIF4-regulated auxin-related genes, enabling their transcriptional activation. Interestingly, this activation also requires the histone deacetylase HDA9, raising the question of how histone deacetylation, typically associated with transcriptional repression, can instead promote gene activation. Here, we identify FVE as a co-regulator that partners with HDA9 to activate PIF4 target genes at elevated temperatures. PIF4 directly interacts with and recruits the FVE-HDA9 complex to its target genes to remove acetylation from histone H4 and H2A.Z. We show that H2A.Z acetylation is required for recruiting the SWR1 complex, which deposits H2A.Z. Consequently, FVE-HDA9-mediated deacetylation reduces SWR1 complex binding and limits H2A.Z deposition. Moreover, we demonstrate that in addition to limiting H2A.Z deposition, H2A.Z depletion also results from H2A.Z eviction mediated by the INO80 complex. Together, these findings uncover a dual mechanism contributing to H2A.Z depletion: INO80-mediated active eviction and histone deacetylation-mediated inhibition of H2A.Z deposition, which underlies PIF4 target gene activation and explain the paradoxical role of histone deacetylation in transcriptional activation.
2026-01-29 | GSE303133 | GEO
Project description:Many plants, including Arabidopsis thaliana, respond to elevated ambient temperatures by altering their growth through a process known as thermomorphogenesis. This response involves the depletion of the repressive histone variant H2A.Z from the gene bodies of PIF4-regulated auxin-related genes, enabling their transcriptional activation. Interestingly, this activation also requires the histone deacetylase HDA9, raising the question of how histone deacetylation, typically associated with transcriptional repression, can instead promote gene activation. Here, we identify FVE as a co-regulator that partners with HDA9 to activate PIF4 target genes at elevated temperatures. PIF4 directly interacts with and recruits the FVE-HDA9 complex to its target genes to remove acetylation from histone H4 and H2A.Z. We show that H2A.Z acetylation is required for recruiting the SWR1 complex, which deposits H2A.Z. Consequently, FVE-HDA9-mediated deacetylation reduces SWR1 complex binding and limits H2A.Z deposition. Moreover, we demonstrate that in addition to limiting H2A.Z deposition, H2A.Z depletion also results from H2A.Z eviction mediated by the INO80 complex. Together, these findings uncover a dual mechanism contributing to H2A.Z depletion: INO80-mediated active eviction and histone deacetylation-mediated inhibition of H2A.Z deposition, which underlies PIF4 target gene activation and explain the paradoxical role of histone deacetylation in transcriptional activation.
2026-01-29 | GSE303142 | GEO