Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis

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Abstract
Trimethylation of histone H3 lysine 27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. We identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways, such as DNA methylation or RNA interference. Unlike in animals, where H3K27m3 occupies large genomic regions, in Arabidopsis, we found that H3K27m3 domains were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low–nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals. During plant and animal development, genes must be activated or repressed according to a strict temporal and spatial schedule. Histones, which are DNA-packaging proteins, play a key role in this process. For development to proceed normally, an amino acid residue (lysine 27) in histone H3 must undergo a chemical modification (called trimethylation). The modified histone (H3K27me3) maintains the repression of its target genes in appropriate tissues or developmental stages. H3K27me3 has been shown to regulate hundreds of genes and many developmental processes in animals, where it also appears to interact with other epigenetic pathways. However, the extent to which this histone modification regulates plant gene expression remained unknown. Does H3K27me3 interact with other epigenetic pathways in plants? Do plants and animals have similar H3K27me3 patterning and underlying mechanisms? To address these questions, we combined chromatin immunoprecipitation with whole-genome tiling microarrays (ChIP-chip) to identify H3K27me3-associated regions across the entire genome of the flowering plant Arabidopsis at high resolution (35 base pairs). The results suggest that H3K27me3 is a major and systematic gene silencing mechanism in plants that acts independently of small RNAs or DNA methylation. Furthermore, distinct features of Arabidopsis H3K27me3 patterning suggest that different mechanisms may be responsible for the establishment and spread of this histone modification in plants and animals.