title: Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis.
abstract: Post-translational chromatin modifications are an important regulatory mechanism in light signalling and circadian clock function. The regulation of diurnal transcript level changes requires fine-tuning of the expression of generally active genes depending on the prevailing environmental conditions. We investigated the association of histone modifications H3K4me3, H3K9ac, H3K9me2, H3S10p, H3K27ac, H3K27me3 and H3S28p with diurnal changes in transcript expression using chromatin immunoprecipitations followed by sequencing (ChIP-Seq) in fully expanded leaves 6 of Arabidopsis thaliana grown in short-day optimal and water-deficit conditions. We identified a differential H3K9ac, H3K27ac and H3S28p signature between end-of-day and end-of-night that is correlated with changes in diurnal transcript levels. Genes with this signature have particular over-represented promoter elements and encode proteins that are significantly enriched for transcription factors, circadian clock and starch catabolic process. Additional activating modifications were prevalent in optimally watered (H3S10p) and in water-deficit (H3K4me3) plants. The data suggest a mechanism for diurnal transcript level regulation in which reduced binding of repressive transcription factors facilitates activating H3K9ac, H3K27ac and H3S28p chromatin modifications. The presence of activating chromatin modification patterns on genes only at times of the day when their expression is required can explain why some genes are differentially inducible during the diurnal cycle.
authors.affiliation: Department of Biology, ETH Zurich, Zurich, 8092, Switzerland. kbaerenfaller@ethz.ch.
authors.forename: Katja
authors.identifier: 0000-0002-1904-9440
authors.initials: K
authors.lastname: Baerenfaller
authors.affiliation: Department of Biology, ETH Zurich, Zurich, 8092, Switzerland.|Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
authors.forename: Huan
authors.initials: H
authors.lastname: Shu
authors.affiliation: Department of Biology, ETH Zurich, Zurich, 8092, Switzerland.
authors.forename: Matthias
authors.initials: M
authors.lastname: Hirsch-Hoffmann
authors.affiliation: Department of Biology, ETH Zurich, Zurich, 8092, Switzerland.
authors.forename: Johannes
authors.initials: J
authors.lastname: Fütterer
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, 8057, Switzerland.
authors.forename: Lennart
authors.initials: L
authors.lastname: Opitz
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, 8057, Switzerland.
authors.forename: Hubert
authors.initials: H
authors.lastname: Rehrauer
authors.affiliation: Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-75007, Sweden.
authors.forename: Lars
authors.initials: L
authors.lastname: Hennig
authors.affiliation: Department of Biology, ETH Zurich, Zurich, 8092, Switzerland. wgruissem@ethz.ch.
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Gruissem
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D002940:Circadian Rhythm; D057890:Epigenomics; D018506:Gene Expression Regulation, Plant; D006657:Histones / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism / Q000502:physiology
chemical_list: D006657:Histones; D012333:RNA, Messenger
keywords: Arabidopsis thaliana; chromatin immunoprecipitation; chromatin modifications; diurnal; epigenetics; histone; leaf