HDA6 Directly Interacts with DNA Methyltransferase MET1 and Maintains Transposable Element Silencing in Arabidopsis

Xuncheng Liu,Koching Wang,Chun-Wei Yu,Ming Luo,Gang Tian,Yuhai Cui,Jun Duan,Keqiang Wu

doi:10.1104/pp.111.184275

Abstract

The molecular mechanism of how the histone deacetylase HDA6 participates in maintaining transposable element (TE) silencing in Arabidopsis (Arabidopsis thaliana) is not yet defined. In this study, we show that a subset of TEs was transcriptionally reactivated and that TE reactivation was associated with elevated histone H3 and H4 acetylation as well as increased H3K4Me3 and H3K4Me2 in hda6 mutants. Decreased DNA methylation of the TEs was also detected in hda6 mutants, suggesting that HDA6 silences the TEs by regulating histone acetylation and methylation as well as the DNA methylation status of the TEs. Similarly, transcripts of some of these TEs were also increased in the methyltransferase1 (met1) mutant, with decreased DNA methylation. Furthermore, H4 acetylation, H3K4Me3, H3K4Me2, and H3K36Me2 were enriched at the coregulated TEs in the met1 and hda6 met1 mutants. Protein-protein interaction analysis indicated that HDA6 physically interacts with MET1 in vitro and in vivo, and further deletion analysis demonstrated that the carboxyl-terminal region of HDA6 and the bromo-adjacent homology domain of MET1 were responsible for the interaction. These results suggested that HDA6 and MET1 interact directly and act together to silence TEs by modulating DNA methylation, histone acetylation, and histone methylation status.

Highlights

The molecular mechanism of how the histone deacetylase HDA6 participates in maintaining transposable element (TE) silencing in Arabidopsis (Arabidopsis thaliana) is not yet defined
Our results indicate that HDA6 and MET1 interact directly and act together to maintain TE silencing by modulating their histone acetylation, methylation, and DNA methylation status
Our previous study revealed that a subset of TEs was up-regulated in axe1-5 and HDA6-RNA interference (RNAi) plants (Yu et al, 2011)

Summary

Introduction

The molecular mechanism of how the histone deacetylase HDA6 participates in maintaining transposable element (TE) silencing in Arabidopsis (Arabidopsis thaliana) is not yet defined. Protein-protein interaction analysis indicated that HDA6 physically interacts with MET1 in vitro and in vivo, and further deletion analysis demonstrated that the carboxyl-terminal region of HDA6 and the bromo-adjacent homology domain of MET1 were responsible for the interaction These results suggested that HDA6 and MET1 interact directly and act together to silence TEs by modulating DNA methylation, histone acetylation, and histone methylation status. HDA6 mutant alleles axe to axe displayed increased expression of the auxin-responsive reporter genes in the absence of auxin treatment, suggesting a role of HDA6 in gene silencing (Murfett et al, 2001) Another hda mutant allele, sil, was identified in a screen for mutations releasing transgene silencing, indicating that HDA6 is required for the maintenance of transcriptional gene silencing (Probst et al, 2004). The molecular mechanism underlying the function of HDA6 in gene silencing is still unclear

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Conclusion