title: Genome invasion by hypo-methylated satellite repeat in Australian crucifer Ballantinia antipoda
organism: Ballantinia antipoda
description: 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.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2018-11-29T17:03:21Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-09-12T18:02:46Z
attributes.tag: External Id
attributes.value: SAMEA4895663
attributes.tag: INSDC center name
attributes.value: MPIPZ COLOGNE
attributes.tag: INSDC first public
attributes.value: 2018-11-29T17:03:21Z
attributes.tag: INSDC last update
attributes.value: 2018-09-12T18:02:46Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: DNASeq_250bp_PE_Bantipoda_run2
attributes.tag: collection date
attributes.value: 2008
attributes.tag: estimated size
attributes.value: 475 000 000
attributes.tag: geographic location (country and/or sea)
attributes.value: Australia
attributes.tag: geographic location (latitude)
attributes.value: -33.002
attributes.tag: geographic location (longitude)
attributes.value: 144.32
attributes.tag: isolation and growth condition
attributes.value: long day
attributes.tag: number of replicons
attributes.value: 6
attributes.tag: plant developmental stage
attributes.value: mature plant
attributes.tag: plant growth medium
attributes.value: soil
attributes.tag: plant structure
attributes.value: leaf
attributes.tag: ploidy
attributes.value: mesoploid
attributes.tag: sample name
attributes.value: DNASeq_250bp_PE_Bantipoda_run2
attributes.tag: scientific_name
attributes.value: Ballantinia antipoda
attributes.tag: source material identifiers
attributes.value: plant