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

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. To investigate the role of SWI3B and HDA6 on transposon silencing, we conducted whole genome bisulfite sequencing (WGBS) from wild-type (Col), swi3b and sil1 mutant plants