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Epigenetic memory mediated by HDA6, Pol IV and Pol V in Arabidopsis.

ABSTRACT: Multiple RNA-sequencing datasets were generated from wild-type Col-0 and hda6, pol IV or pol V null mutant samples to dissect genetic requirements for the maintenance of epigenetic memory and silent locus identity in Arabidopsis thaliana.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Craig Pikaard

PROVIDER: E-MTAB-4337 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A two-step process for epigenetic inheritance in Arabidopsis.

Blevins Todd T Pontvianne Frédéric F Cocklin Ross R Podicheti Ram R Chandrasekhara Chinmayi C Yerneni Satwica S Braun Chris C Lee Brandon B Rusch Doug D Mockaitis Keithanne K Tang Haixu H Pikaard Craig S CS

Molecular cell 20140320 1

In Arabidopsis, multisubunit RNA polymerases IV and V orchestrate RNA-directed DNA methylation (RdDM) and transcriptional silencing, but what identifies the loci to be silenced is unclear. We show that heritable silent locus identity at a specific subset of RdDM targets requires HISTONE DEACETYLASE 6 (HDA6) acting upstream of Pol IV recruitment and siRNA biogenesis. At these loci, epigenetic memory conferring silent locus identity is erased in hda6 mutants such that restoration of HDA6 activity ...[more]

PMID: 24657166

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RNA-seq of 14 days old arabidopsis in Col hda6 ldl1/2 and hda6/ldl1/2

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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

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Expression analysis in HDA6 mutants

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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.

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