Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance

Abstract

Nucleolar dominance describes the silencing of one parental set of ribosomal RNA (rRNA) genes in a genetic hybrid, an epigenetic phenomenon that occurs on a scale second only to X-chromosome inactivation in mammals. An RNA interference (RNAi) knockdown screen revealed that the predicted Arabidopsis histone deacetylase, HDA6, is required for rRNA gene silencing in nucleolar dominance. In vivo, derepression of silenced rRNA genes upon knockdown of HDA6 is accompanied by nucleolus organizer region (NOR) decondensation, loss of promoter cytosine methylation, and replacement of histone H3 Lys 9 (H3K9) dimethylation with H3K4 trimethylation, H3K9 acetylation, H3K14 acetylation, and histone H4 tetra-acetylation. Consistent with these in vivo results, purified HDA6 deacetylates lysines modified by histone acetyltransferases whose substrates include H3K14, H4K5, and H4K12. HDA6 localizes, in part, to the nucleolus, supporting a model whereby HDA6 erases histone acetylation as a key step in an epigenetic switch mechanism that silences rRNA genes through concerted histone and DNA modifications.

Arabidopsis histone deacetylase 6: a green link to RNA silencing

“…oregonstate.edu/db/). The roles of these siRNAs in AtHDA6-controlled regional or long-range silencing of rDNA repeats have not been addressed so far (Probst et al, 2004;Lawrence et al, 2004;Earley et al, 2006). In summary, compared to other Arabidopsis RPD3-type HDACs, AtHDA6 shows preponderance for the involvement in silencing processes that are likely controlled by dsRNA, which is in agreement with the proposed functional diversification within this family (Pandey et al, 2002).…”

“…In agreement with this hypothesis, endogenous regulatory functions of AtHDA6 have so far only been linked to the regulation of chromatin at recombinant DNA (rDNA) loci, where Athda6 alleles have been shown to cause decreased CpG methylation as well as localized enhanced histone acetylation (Probst et al, 2004). Furthermore, AtHDA6 has been characterized as a broad range HDAC that is necessary for nucleolar dominance, a long-range repression of rDNA specifically from one parent in allopolyploid hybrids (Earley et al, 2006). AtHDA5, AtHDA15 and AtHDA18 are members of the class II, HDA1-related group of HDACs.…”

“…Interestingly, an extensive search for AtHDA6-interacting proteins by yeast two-hybrid analyses identified two RNA-binding proteins and an RNA helicase (Stoiber and Aufsatz, unpublished results). All three proteins are annotated to localize to the nucleolus, and thus potentially colocalize in planta with AtHDA6, for which nucleolar localization has been reported (Earley et al, 2006), as well as with components of the processing machinery of nuclearacting siRNAs Li et al, 2006b). Although the repression of a transgene RdDM target promoter can not be maintained in mutants affecting DNA methylation (see above), which challenges the hypothesis of methylation-independent recruitment pathways, it should be kept in mind that silencing in the two-component RdDM model system is triggered by RNA signals, which are supplied in trans.…”

Characterization of AtNUC-L1 Reveals a Central Role of Nucleolin in Nucleolus Organization and Silencing of AtNUC-L2 Gene in Arabidopsis

“…Chromatin is generally considered as a prerequisite for transcriptional activation, in such a way that the amount of decondensed chromatin is taken as a marker of the gene expression activity, either real or potential. The decondensation of rDNA has no discernible effect on rRNA mature transcripts level, as observed in the HDA6 mutant (Earley et al, 2006). One explanation would be that increased rRNA gene transcription is undetectable.…”

rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch

“…These observations have been extended to include additional modifications that help define the on and off states of rRNA genes, as summarized in Figure 3. For instance, in addition to H3K4me3, active rRNA genes are hyperacetylated on lysines 5, 8, 12 and 16 of histone H4 and on lysines 9 and 14 of histone H3 whereas inactive genes are depleted for these modifications [46].Importantly, DNA methylation and histone modification states are interdependent and mutually reinforcing at rRNA genes. This was initially shown by experimentally turning on silenced rRNA genes using either aza-dC or TSA and showing that treatment with either chemical has identical consequences with respect to the suite of DNA and histone modifications that ensue [40].…”