Natural Variation of H3K27me3 Distribution Between Two Arabidopsis Accessions and its Association with Flanking Transposable Elements

We analyzed the extent of natural variation of Histone H3 lysine 27 trimethylation (H3K27me3) in two accessions of Arabidopsis thaliana, Landsberg erecta (Ler) and Columbia (Col), and their hybrids using chromatin immunoprecipitation followed by microarray or sequencing analysis (ChIP-chip and ChIP-seq). H3K27me3 and histone 3 lysine 9 dimethylation (H3K9me2) are two independent repressive chromatin modifications. A computational workflow was implemented that includes remapping of microarray probes to the Col and Ler genome assemblies in order to exclude differential signals due to genome polymorphisms.

The majority of genes that are H3K27me3 targets in Col are also targets in Ler and the F1 of reciprocal crosses. Stringent detection of differentially methylated targets results in few Ler specific H3K27me3 targets. These were validated with independent ChIP-PCR. Ler specific targets show allele-specific H3K27me3 in both hybrids, consistent with a cis-regulatory mechanism for establishing H3K27me3.

Ler-specific H3K27me3 targets fall into two groups. Five were actively expressed and marked by H3K4me3 in Col. However, for the majority of Ler-specific H3K27me3 targets no expression can be detected in Col, Ler or 17 other Arabidopsis accessions. Instead of H3K27me3, H3K9me2 and other repressive marks such as DNA methylation were observed at these loci in Col. Frequently, transposable elements were found neighboring these loci in Col, and in many cases these transposable elements are missing in the Ler genome assembly. We propose a model where a transposon insertion specific to Col results in recruitment of H3K9me2, which spreads to neighboring genes already in a repressed state through H3K27me3, resulting in Ler specific H3K27me3 as the ancestral state.