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HDA6 mediated euchromatic silencing acts independently of DNA methylation

ABSTRACT: Transcriptome of epic1 (hda6-8) a weak allele of HDA6 that does not affect DNA methylation

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE65640 | GEO | 2015/03/11

SECONDARY ACCESSION(S): PRJNA274572

REPOSITORIES: GEO

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SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis

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.

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Genome-wide maps of H3Ac in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3Ac in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide H3AC levels of 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP was performed using anti-H3K9K14Ac antibody (Millipore; 06-599), and ChIP DNA were analyzed by Illumina HiSeq 2500.

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Plastid signaling triggers HDA6-mediated epigenetic programs during environmental sensing in plants [Bisulfite-seq]

Project description:Plants adapt to environmental changes by adjusting growth and defense, and the role of epigenetic modifications in this process is unclear. Sensing and adjusting to environmental changes are more important in certain tissues such as epidermis, vasculature, meristem, and reproductive tissues. These tissues possess sensory plastids that are specialized in environmental sensing. We show perturbation of four sensory plastid proteins MSH1, PPD3, CUE1, and SAL1 induce gene expression and DNA methylation changes targeted to networks associated to environmental sensing, with significant overlap with hda6-induced CHG hypermethylated genes at 12-hr daylength. At 16-hr daylength, hda6 loses CHG hypermethylation in gene body, and sensory plastid mutants have weaker phenotypes and DNA methylation- and gene expression- associated gene networks. We show daylength-responsive epistatic interaction between sensory plastid mutants with hda6. We also show that hda6 mutation confers daylength memory and, with msh1, enhanced tolerance to heat stress and biotic stress. These results suggest that HDA6 mediates programmed adjustments in plant phenotype triggered by sensory plastid-to-nucleus retrograde signaling in response to daylength and environmental cues.

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Plastid signaling triggers HDA6-mediated epigenetic programs during environmental sensing in plants [RNA-seq]

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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.

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The Histone Deacetylases HDA6 and HDA9 coordinately regulate valve cell elongation through depressing auxin signaling in Arabidopsis

Project description:Both of Histone Deacetylases HDA6 and HDA9 belong to RPD3/HDA1 class I subfamily, and they have similar protein structure. Loss of function of HDA9 display a blunt silique. Although there is not protein-protein interaction between HDA6 and HDA9, they simultaneously loss function led to “nock-shape” silique that more seriously silique phenotype than hda9. The silique valve cell of hda9 and hda6 hda9 were longer than wild type and hda6. The transcripts level of auxin signaling related genes were mis-regulated in hda9 and hda6 hda9 silique, and GFP signaling derived by auxin response promoter DR5 were weaker in hda9 and hda6 hda9 than wild type and hda6. Thus, our findings reveal that HDA6 and HDA9 coordinately control silique valve cell elongation through affecting auxin signaling related genes expression in silique.

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Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [WGBS]

Project description:Histone deacetylases (HDAs) are evolutionally conserved enzymes and often form a multiprotein complex with histone Lysine-Specific Demethylase 1 (LSD1) to play central roles in epigenetic silencing in yeast and animals. In Arabidopsis, either HDA6 or LSD1-LIKE 1 and 2 (LDL1/2) are known to silence transposable element (TE), but their joint effect remains unexplored. Here, we revealed the individual and joint effects of HDA6 and LDL1/2 carefully by examining the transcriptomes, the genome wide distribution of H3Ac, H3K4me2, and DNA methylation in wildtype and mutants (hda6, ldl1/2 and hda6/ldl1/2). We found that HDA6 silenced 517 TEs by itself, LDL1/2 silenced 2 TEs alone and HDA6 silenced 15 TEs in cooperation with LDL1/2; suggesting that HDA6 has a stronger impact on TE silencing than LDL1/2; the effect of HDA6 is mostly independent of LDL1/2 whereas most LDL1/2 effect requires HDA6. Also, we observed that the expression of TE showed clear synergistic (enhanced de-repression in hda6/ldl1/2) and antagonistic (lower de-repression in hda6/ldl1/2) effects at different sets of TEs. Further analysis showed that the TEs targeted by either of the two effects exhibited totally different epigenome patterns.

2024-11-06 | GSE216787 | GEO

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