Abstract
In plants, RNA-directed DNA methylation (RdDM) and related transcriptional gene silencing (TGS) involve members of the suppressor of variegation 3-9-homologous (SUVH) group of putative histone methyltransferases. Utilizing a reverse genetic approach in Arabidopsis thaliana, we demonstrate that two closely related SUVH members, SUVH2 and SUVH9, act partially non-redundant in RdDM. DNA methylation, transcript accumulation and association with histone modifications were analyzed at the endogenous RdDM target AtSN1 (a SINE-like retroelement) in suvh2 and suvh9 single as well as suvh2 suvh9 double mutants. SUVH2 was found to be required for full DNA methylation at AtSN1 in early seed development and was also higher expressed in seeds than at later developmental stages. SUVH9 had its impact on RdDM later during vegetative development of the plant and was also higher expressed during that stage than at earlier developmental stages. The strongest reduction of RdDM at AtSN1 was found in suvh2 suvh9 double mutant plants. Histone 3-lysine 9-dimethylation (H3K9me2) associated with AtSN1 was reduced only in the simultaneous absence of functional SUVH2 and SUVH9. Thus, SUVH2 and SUVH9 functions in RdDM and TGS are overlapping in spite of some developmental specialization. Pol V specific transcripts were reduced in suvh2 suvh9 plants. This might indicate a role of these SUVH proteins in Pol V complex recruitment.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-012-9934-x) contains supplementary material, which is available to authorized users.
Highlights
SET domain containing proteins can be divided into four different classes typified by the corresponding proteins of Drosophila E(Z), TRX, ASH1 and SU(VAR)3-9 (Baumbusch et al 2001; Thorstensen et al 2011)
Utilizing a reverse genetic approach in Arabidopsis thaliana, we demonstrate that two closely related suppressor of variegation 3-9homologous (SUVH) members, SUVH2 and SUVH9, act partially non-redundant in RNA-directed DNA methylation (RdDM)
SUVH2 and SUVH9 are differentially expressed during A. thaliana development
Summary
SET domain containing proteins can be divided into four different classes typified by the corresponding proteins of Drosophila E(Z), TRX, ASH1 and SU(VAR) (Baumbusch et al 2001; Thorstensen et al 2011). SUVH2 (encoded by At2g33290) and SUVH9 (encoded by At4g13460), show considerable sequence similarity (Naumann et al 2005) and form a subgroup within the SUVH-family that is characterized by the absence of the catalytically important postSET domain (Rea et al 2000). The SET domain is essential for histone methyltransferase activity (Rea et al 2000). SUVH4, SUVH5 and SUVH6 readily methylate bovine H3 (Jackson et al 2004; Ebbs and Bender 2006). SUVH5 showed some activity on bovine H2A (Ebbs and Bender 2006). SUVH2 has been reported to methylate H4 in one study using reconstituted recombinant nucleosomes
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