Genome invasion by hypo-methylated satellite repeat in Australian crucifer Ballantinia antipoda

Repetitive sequences are ubiquitous components of eukaryotic genomes, which contribute to the regulation of transcription and genome evolution. To prevent their uncontrolled and largely negative activity, they are embedded in the repressive heterochromatic environment rich in DNA methylation. Here, we analyzed the sequence composition and the epigenetic makeup of a peculiar non-pericentromeric DNA methylation-poor heterochromatic segments in the genome of the Australian crucifer Ballantinia antipoda. By combination of high throughput sequencing, graph-based clustering and cytogenetics, we found that the heterochromatic segments consist of a mixture of unique sequences and an A-T rich 177 bp satellite repeat (BaSAT1), which occupies about 10% of B. antipoda nuclear genome in >250,000 copies. Individual copies show a surprising variation in DNA methylation and repressive histone methylation, which appears to be genetically pre-determined. BaSAT1 repeats containing cytosines in the symmetric context (CG or CHG, where H is A, T or C) are fully methylated, while those having cytosines exclusively in the asymmetric (CHH) configuration are free of both DNA methylation and H3K9me2. This shows that the presence or the absence of repressive epigenetic marks is determined primarily genetically, and that the cytosines in symmetric sequence context are required for efficient and long-term DNA methylation of tandem repeats in plants.