Arabidopsis thaliana
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PROVIDER: PRJNA274572 | ENA |
REPOSITORIES: ENA
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Project description:DNA cytosine methylation is a hallmark of epigenetic gene silencing. DNA demethylation requires ROS1, a bifunctional DNA glycosylase/lyases and open chromatin status mediated by IDM1. HDA6 is a RDP3-like histone deacetylase and was confirmed to mediate DNA methylation. In previous screening for ros1 suppressor, we identified two hda6 mutants reverting ros1-caused hypermethylation at RD29A and 35S promoters respectively, indicating the antagonization of DNA methylation between HDA6 and ROS1. To learn antagonized effects between HDA6 and ROS1 at DNA cytosine methylation genome-wide, we performed whole genome bisulfite sequencing to search antagonized targets of HDA6 and ROS1 and their specific targets to evaluate their roles on DNA methylation. To evaluate HDA6’s roles in sRNA biogenesis and nucleosome positioning, we also performed small RNA sequencing and genome-wide mapping of nucleosome positioning of C24, ros1, hda6-9 and hda6-10. Our results indicate that around 43% ros1-caused CG hypermethylation, 74.5% and 84.5% ros1-caused CHG and CHH hypermethylation were reverted by the two hda6 alleles in the ros1 background respectively. These results indicate that most of ROS1-demethylated targets are also HDA6-mediated DNA methylated targets. In addition, we observed that HDA6-affected DNA methylation targets are far more than ROS1-demethylation targets at CHG and CHH context, but not at CG context. sRNA analysis showed that HDA6 inhibits LTR/Gypsy and TE gene 24nt siRNA accumulation, while promotes RC/Helitron 24nt siRNA accumulation. Our Mono-nucleosome positioning data further showed that the two hda6 alleles have striking difference on nucleosome positioning, hda6-10 obviously have different nucleosome positioning patterns with hda6-9. Our results indicate HDA6 not only mediates overall DNA methylation at CG, CHG and CHH context, and antagonizes with ROS1 mediated DNA demethylation, but also regulates nucleosome positioning and small RNA accumulation at some genome specific regions.
2021-07-07 | GSE136193 | GEO
Project description:Although the interplay of covalent histone acetylation/deacetylation and ATP-dependent chromatin remodeling is crucial for the regulation of chromatin structure and gene expression in eukaryotes, the underlying molecular mechanism in plants remains largely unclear. Here we show a direct interaction between Arabidopsis SWI3B, an essential subunit of the SWI/SNF chromatin-remodeling complex, and the RPD3/HDA1-type histone deacetylase HDA6 both in vitro and in vivo. Furthermore, SWI3B and HDA6 co-repress the transcription of a subset of transposons. Both SWI3B and HDA6 maintain transposon silencing by decreasing histone H3 acetylation but increasing histone H3 lysine 9 di-methylation, DNA methylation and nucleosome occupancy. Our findings reveal that SWI3B and HDA6 may act in the same corepressor complex to maintain transposon silencing in Arabidopsis.
2021-06-20 | GSE133235 | GEO
Project description:HDA6 is a RPD3-like histone deacetylase. In Arabidopsis, it mediates transgene and some endogenous target transcriptional gene silencing (TGS) via histone deacetylation and DNA methylation. Here, we characterized two hda6 mutant alleles that were recovered as second-site suppressors of the DNA demethylation mutant ros1-1. Although both alleles derepressed 35S::NPTII and RD29A::LUC in the ros1-1 background, they had distinct effects on the expression of these two transgenes. In accordance to expression profiles of two transgenes, the alleles have distinct opposite methylation profiles on two reporter gene promoters. Furthermore, both alleles could interact in vitro and in vivo with the DNA methyltransferase1 with differential interactive strength and patterns. Although these alleles accumulated different levels of repressive/active histone marks, DNA methylation but not histone modifications in the two transgene promoters was found to correlate with the level of derepression of the reporter genes between the two had6 alleles. Our study reveals that mutations in different domains of HDA6 convey different epigenetic status that in turn controls the expression of the transgenes as well as some endogenous loci.
2016-10-01 | GSE73716 | GEO
Project description:A SWI/SNF nucleosome remodeling complex acts in non-coding RNA-mediated transcriptional silencing
| PRJNA167967 | ENA
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
Project description:RNA silencing is a mechanism for regulating gene expression at the transcriptional and post-transcriptional levels. Its functions include regulating endogenous gene expression and protecting the cell against viruses and invading transposable elements (TEs). A key component of the mechanism is small RNAs (sRNAs) of 21-24 nucleotides (nt) in length, which direct the silencing machinery in a sequence specific manner to target nucleic acids. sRNAs of 24 nt are involved in methylation of cytosine residues of target loci in three sequence contexts (CG, CHG and CHH), referred to as RNA-directed DNA methylation (RdDM). We previously demonstrated that 24 nt sRNAs are mobile from shoot to root in Arabidopsis thaliana. In this study we demonstrated that methylation of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot. Furthermore, we found that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. These findings were made using base-resolution next generation sequencing approaches and genome wide analyses. Specific classes of short TEs are the predominant targets of mobile sRNA-dependent DNA methylation; classes typically found in gene-rich euchromatic regions. Mobile sRNA-regulated genes were also identified. Mechanistically, we demonstrate that mobile sRNA-dependent non-CG methylation is largely independent of the CMT2/3 RdDM pathway but dependent upon the DRM1/DRM2 RdDM pathway. This is in contrast to non-mobile sRNA-dependent DNA methylation, which predominantly depends upon the CMT2/3 RdDM pathway. These data are complementary to the small RNA sequencing data from Arabidopsis root grafts described in Molnar et al (Science, 2010 May 14;328(5980):872-5).
2016-01-04 | E-MTAB-3473 | biostudies-arrayexpress
Project description:In addition to the canonical RNAi pathways that targets mRNAs in the cytoplasm, several RNA-dependent pathways operate in the nucleus to induce sequence-specific epigenetic modifications. One specialized type of RNAi-mediated pathway is RNA-directed DNA methylation (RdDM). During RdDM, nuclear DNA with sequence identity to the trigger dsRNA is de novo methylated at almost all cytosine residues, providing a mark for the formation of transcriptionally silent heterochromatin. Genetic forward screens identified the RPD3-like histone deacetylase HDA6 as the enzyme responsible for the histone deacetylation step of RdDM and suggest that HDA6 might have acquired specific functions for RNA-directed transcriptional silencing processes [Aufsatz et al., 2002a; Aufsatz et al., 2002b]. Complete loss-of-function mutants for AtHDA6 (rts1-1; RNA-mediated transcriptional gene silencing) exhibit reactivation of RdDM-silenced promoters, despite the continuous presence of the silencing-inducing RNA signal. One of the found mutant alleles, rts1-5, has an amino acid substitution located at a conserved position within the HDAC domain (Naumann et al., manuscript in preparation). This mutant is characterized by strong reactivation of an RdDM-silenced target promoter, despite maintaining wild-type levels of cytosine methylation. An evaluation of the transcription pattern among the mutants with opposite methylation phenotype and wild-type plants should show which genes are differentially regulated between the mutants in comparison to wild-type plants. Keywords: Expression profiling by array 9 samples were used in this experiment
2009-11-17 | E-GEOD-18988 | biostudies-arrayexpress
Project description:DNA methylation is an important epigenetic modification involved in many biological processes, and active DNA demethylation plays critical roles in regulating expression of genes and anti-silencing of transgenes. In this study, we isolated mutations in one arabidopsis gene, ROS5, which causes the silencing of transgenic 35S-NPTII because of DNA hypermethylation, but no effect on transgenic RD29A-LUC. ROS5 encodes an atypical small heat shock protein. ROS5 can physically interact with IDM1 and is required for preventing DNA hypermethylation of some endogenous genes that are also regualated by IDM1 and ROS1. We propose that ROS5 may regulate active DNA demethylation by interacting with IDM1, thereby creating a friendly chromatin environment that facilitates the binding of ROS1 to erase DNA methylation.
2014-08-28 | E-MTAB-4323 | biostudies-arrayexpress
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of HDA6 in 14 days old arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide HDA6-binding maps of 14 days old arabidopsis. To reveal bound genes by HDA6, chimeric protein HDA6-GFP was expressed under HDA6 promoter in hda6 (HDA6pro:HDA6:GFP/ hda6). ChIP was performed using anti-GFP antibody (ab290; ABCAM), and ChIP DNA were analyzed by Illumina HiSeq 2500.
2021-03-30 | GSE132563 | GEO
Project description:Loss of H3K27 monomethylation leads to DNA-methylation-independent release of gene silencing
| PRJNA115495 | ENA