Mutation of Arabidopsis SMC4 identifies condensin as a corepressor of pericentromeric transposons and conditionally expressed genes
- Jing Wang1,2,
- Todd Blevins1,2,3,6,
- Ram Podicheti4,5,
- Jeremy R. Haag7,
- Ek Han Tan8,
- Feng Wang1,2 and
- Craig S. Pikaard1,2,3
- 1Department of Biology, Indiana University, Bloomington, Indiana, 47405, USA;
- 2Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, 47405, USA;
- 3Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana, 47405, USA;
- 4Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, 47405, USA;
- 5School of Informatics and Computing, Indiana University, Bloomington, Indiana, 47405, USA
- Corresponding author: cpikaard{at}indiana.edu
Abstract
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.
Keywords
- DNA methylation
- SMC proteins
- chromosome condensation
- epigenetic regulation
- gene silencing
- heterochromatin formation
Footnotes
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Supplemental material is available for this article.
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Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.301499.117.
- Received May 5, 2017.
- Accepted August 7, 2017.
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