Skip to content

Research at St Andrews

Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance

Research output: Contribution to journalArticle

DOI

Open Access permissions

Open

Author(s)

Katie Baker, Taniya Dhillon, Isabelle Colas, Nicola Cook, Iain Milne, Linda Milne, Micha Bayer, Andrew J. Flavell

School/Research organisations

Abstract

Combinations 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.
Close

Details

Original languageEnglish
Pages (from-to)111–124
JournalThe Plant Journal
Volume84
Issue number1
Early online date9 Sep 2015
DOIs
Publication statusPublished - Oct 2015

    Research areas

  • Epigenomics, Heterochromatin, Pericentromeric, Chromatin immunoprecipitation next-generation sequencing, Histone modification, Barley, Hordeum vulgare, PRJEB8068

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Genomics of sex allocation in the parasitoid wasp Nasonia vitripennis

    Pannebakker, B. A., Cook, N., van den Heuvel, J., van de Zande, L. & Shuker, D. M., 20 Jul 2020, In : BMC Genomics. 21, 14 p., 499.

    Research output: Contribution to journalArticle

  2. Validating the demethylating effects of 5-aza-2'-deoxycytidine in insects requires a whole-genome approach (A reply to Ellers et al.)

    Cook, N., Parker, D. J., Tauber, E., Pannebakker, B. A. & Shuker, D. M., Sep 2019, In : American Naturalist. 194, 3

    Research output: Contribution to journalArticle

  3. Local mate competition modifies the costs of mating in a mostly monandrous parasitoid wasp

    Boulton, R. A., Cook, N., Greenway, E. V., Glaser, G. L., Green, J. & Shuker, D. M., 5 Apr 2019, In : Behavioral Ecology. 30, 2, p. 417-425 9 p.

    Research output: Contribution to journalArticle

  4. Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis

    Cook, N., Boulton, R., Green, J., Trivedi, U., Tauber, E., Pannebakker, B. A., Ritchie, M. G. & Shuker, D. M., Feb 2018, In : Royal Society Open Science. 5, 8 p., 171718.

    Research output: Contribution to journalArticle

  5. Sperm blocking is not a male adaptation to sperm competition in a parasitoid wasp

    Boulton, R. A., Cook, N., Green, J., Greenway, E. V. & Shuker, D. M., 13 Jan 2018, In : Behavioral Ecology. 29, 1, p. 253-263

    Research output: Contribution to journalArticle

Related by journal

  1. Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari

    Pokhare, S. S., Thorpe, P., Hedley, P., Morris, J., Habash, S. S., Elashry, A., Eves-van den Akker, S., Grundler, F. M. W. & Jones, J., 17 Aug 2020, In : The Plant Journal. 103, 4, p. 1263-1274 12 p.

    Research output: Contribution to journalArticle

  2. TERMINAL FLOWER-1/CENTRORADIALIS inhibits tuberization via protein interaction with the tuberigen activation complex

    Zhang, X., Campbell, R., Ducreux, L. J. M., Morris, J., Hedley, P. E., Mellado-Ortega, E., Roberts, A. G., Stephens, J., Bryan, G. J., Torrance, L., Chapman, S. N., Prat, S. & Taylor, M. A., 14 Jul 2020, In : The Plant Journal. Early View, 16 p.

    Research output: Contribution to journalArticle

  3. The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

    Baker, K., Bayer, M., Cook, N., Dressig, S., Dhillon, T., Russell, J., Hedley, P. E., Morris, J., Ramsay, L., Colas, I., Waugh, R., Steffenson, B., Milne, I., Stephen, G., Marshall, D. & Flavell, A. J., Sep 2014, In : The Plant Journal. 79, 6, p. 981-992 12 p.

    Research output: Contribution to journalArticle

  4. Live-cell imaging of viral RNA genomes using a Pumilio-based reporter

    Tilsner, J., Linnik, O., Christensen, N. M., Bell, K., Roberts, I. M., Lacomme, C. & Oparka, K. J., Feb 2009, In : The Plant Journal. 57, 4, p. 758-770 13 p.

    Research output: Contribution to journalArticle

ID: 216108269

Top