title: Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation.
abstract: RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602.
authors.forename: Jonathan I
authors.initials: JI
authors.lastname: Gent
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306.
authors.forename: Thelma F
authors.initials: TF
authors.lastname: Madzima
authors.affiliation: Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands.
authors.forename: Rechien
authors.initials: R
authors.lastname: Bader
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Kent
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands.
authors.forename: Maike
authors.initials: M
authors.lastname: Stam
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306.
authors.forename: Karen M
authors.initials: KM
authors.lastname: McGinnis
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602 Department of Genetics, University of Georgia, Athens, Georgia 30602.
authors.forename: R Kelly
authors.initials: RK
authors.lastname: Dawe
mesh_terms: D002503:Centromere / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D019175:DNA Methylation; D018744:DNA, Plant / Q000737:chemistry*; D022041:Euchromatin / Q000378:metabolism; D020868:Gene Silencing; D018745:Genome, Plant; D006570:Heterochromatin / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D034741:RNA, Small Interfering / Q000502:physiology; D003313:Zea mays / Q000235:genetics*
chemical_list: D002843:Chromatin; D018744:DNA, Plant; D022041:Euchromatin; D006570:Heterochromatin; D006657:Histones; D034741:RNA, Small Interfering