The plant Topoisomerase VI complex has been implicated in a wide array of biological processes but little is known about its precise molecular role. In this study, we provide evidence that Topo VI acts as a chromatin barrier between chromatin territories by interacting with methionine adenosyltransferases (MAT), which produce the universal donor of methyl groups S-adenosyl-methionine (SAM). We first show that pericentromeric transposable elements (TEs) are awakened whereas euchromatic island genes (EIGs) within heterochromatin are downregulated in mutants of the Topo VI complex. Consistent with this, the level of repressive H3K9me2 marks increases at EIGs loci while it decreases at TEs in a hypomorphic Topo VI mutant. We demonstrate that the Topo VI complex can interact with the SAM synthase MAT3 and drives it to TEs. A deficiency of Topo VI induces relocation of MAT3 from TEs to EIGs islands, leading to the levelling of the H3K9me2 mark and hence heterochromatin spreading. Overall design: The transcriptome analysis of the caa39 mutant comprises three biological replicates for mutant and WT genotypes. The ChiPseq analysis of H3K9me2 includes a comparison of a pool of two biological replicates for caa39 and wt. This was done in duplicate for H3K27me3. In addition, an input chromatin control comprising a pool of two biological replicates was used for both genotypes. In total, we analyzed 6 RNAseq samples, and 6 ChIP samples and 2 input chromatin samples.