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Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes

In this study, Wang et al. perform genome-wide analyses that implicate condensin in the suppression of hundreds of loci, acting in both DNA methylation-dependent and methylation-independent pathways. They show that silencing of transposons in the pericentromeric heterochromatin of Arabidopsis thaliana requires SMC4, a core subunit of condensins I and II, acting in conjunction with CG methylation by MET1, CHG methylation by CMT3, the chromatin remodeler DDM1, and histone modifications, including H3K27me1, imparted by ATXR5 and ATXR6.

In eukaryotes, transcriptionally inactive loci are enriched within highly condensed heterochromatin. In plants, as in mammals, the DNA of heterochromatin is densely methylated and wrapped by histones displaying a characteristic subset of post-translational modifications. Growing evidence indicates that these chromatin modifications are not sufficient for silencing. Instead, they are prerequisites for further assembly of higher-order chromatin structures that are refractory to transcription but not fully understood. We show that silencing of transposons in the pericentromeric heterochromatin of Arabidopsis thaliana requires SMC4, a core subunit of condensins I and II, acting in conjunction with CG methylation by MET1 (DNA METHYLTRANSFERASE 1), CHG methylation by CMT3 (CHROMOMETHYLASE 3), the chromatin remodeler DDM1 (DECREASE IN DNA METHYLATION 1), and histone modifications, including histone H3 Lys 27 monomethylation (H3K27me1), imparted by ATXR5 and ATXR6. SMC4/condensin also acts within the mostly euchromatic chromosome arms to suppress conditionally expressed genes involved in flowering or DNA repair, including the DNA glycosylase ROS1, which facilitates DNA demethylation. Collectively, our genome-wide analyses implicate condensin in the suppression of hundreds of loci, acting in both DNA methylation-dependent and methylation-independent pathways.

MORC proteins and epigenetic regulation

Two recent studies in Arabidopsis implicated MORC proteins, which contain a GHKL ATPase domain, in transcriptional gene silencing. Here, these studies are compared and contrasted to discuss the roles of MORC proteins in epigenetic regulation. Although MORC proteins are likely to catalyze changes in chromatin structure in response to epigenetic signals, their precise mode of action and target site-specificity still remain unclear.