The chromatin landscape of the barley genome reveals unexpected genome-level features linked with H3K27me3 and the distributions of transposable element families

We have determined the genomic and genic targets for nine modified histones from the developing barley seedling. We have analysed peak sharing relationships and distribution patterns at both the gene and genome level to explore the relationships among these chromatin marks. Eight out of nine histone modifications fall into four genomic distribution classes that map exactly onto three peak-sharing categories, showing that the overlaps among these chromatin marks at the local level are tightly aligned with their corresponding chromosomal distributions. When we related the genomic locations of these modifications to the genomic landscape of barley we discovered unexpected differences in histone profiles between TE classes that relate to the different distributions of these elements in the genome. We have used the peak sharing data to define a set of 10 chromatin states which represent the various local chromatin environments from the actively expressed gene at one end to repressed heterochromatin at the other. When these states were mapped against the barley genome we observed that both gene-rich chromosome arms of every barley chromosome are divided into two distinct regions. The first of these is a telomere-proximal region, within which H3K27me3-bearing states cover both genes and the surrounding intergenic repetitious DNA. Adjacent to this region the remainder of the gene-rich predominantly euchromatic arms are characterised by active chromatin states lacking H3k27me3. Lastly,we have created an web genome browser, which makes these data available to facilitate future study of the cereal epigenome.