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dc.contributor.authorBaker, Katie
dc.contributor.authorDhillon, Taniya
dc.contributor.authorColas, Isabelle
dc.contributor.authorCook, Nicola
dc.contributor.authorMilne, Iain
dc.contributor.authorMilne, Linda
dc.contributor.authorBayer, Micha
dc.contributor.authorFlavell, Andrew J.
dc.identifier.citationBaker , K , Dhillon , T , Colas , I , Cook , N , Milne , I , Milne , L , Bayer , M & Flavell , A J 2015 , ' Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance ' , The Plant Journal , vol. 84 , no. 1 , pp. 111–124 .
dc.identifier.otherPURE: 216108269
dc.identifier.otherPURE UUID: 94c7fde8-74b6-4385-9ef1-872f6661d5a3
dc.identifier.otherBibtex: urn:c6b430487fac6d84e2e9a99134f9dfc0
dc.identifier.otherScopus: 84942815994
dc.identifier.otherORCID: /0000-0003-4462-0116/work/60427605
dc.descriptionThis work was supported by grant BBSRC BB/I1022899/1 ‘The diversity and evolution of the gene component of the barley pericentromeric heterochromatin’.en
dc.description.abstractCombinations of histones carrying different covalent modifications are a major component of epigenetic variation. We have mapped nine modified histones in the barley seedling epigenome by chromatin immunoprecipitation next-generation sequencing (ChIP-seq). The chromosomal distributions of the modifications group them into four different classes, and members of a given class also tend to coincide at the local DNA level, suggesting that global distribution patterns reflect local epigenetic environments. We used this peak sharing to define 10 chromatin states representing local epigenetic environments in the barley genome. Five states map mainly to genes and five to intergenic regions. Two genic states involving H3K36me3 are preferentially associated with constitutive gene expression, while an H3K27me3-containing genic state is associated with differentially expressed genes. The 10 states display striking distribution patterns that divide barley chromosomes into three distinct global environments. First, telomere-proximal regions contain high densities of H3K27me3 covering both genes and intergenic DNA, together with very low levels of the repressive H3K27me1 modification. Flanking these are gene-rich interior regions that are rich in active chromatin states and have greatly decreased levels of H3K27me3 and increasing amounts of H3K27me1 and H3K9me2. Lastly, H3K27me3-depleted pericentromeric regions contain gene islands with active chromatin states separated by extensive retrotransposon-rich regions that are associated with abundant H3K27me1 and H3K9me2 modifications. We propose an epigenomic framework for barley whereby intergenic H3K27me3 specifies facultative heterochromatin in the telomere-proximal regions and H3K27me1 is diagnostic for constitutive heterochromatin elsewhere in the barley genome.
dc.relation.ispartofThe Plant Journalen
dc.rights© 2015 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License (, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.en
dc.subjectChromatin immunoprecipitation next-generation sequencingen
dc.subjectHistone modificationen
dc.subjectHordeum vulgareen
dc.subjectQH301 Biologyen
dc.titleChromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundanceen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.contributor.institutionUniversity of St Andrews. Centre for Biological Diversityen
dc.description.statusPeer revieweden

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