title: Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants.
abstract: The fundamental unit of chromatin is the nucleosome that consists of a protein octamer composed of the four core histones (Hs; H3, H4, H2A, and H2B) wrapped by 147 bp of DNA. Nucleosome occupancy and positioning have proven to be dynamic and have a critical impact on expression, regulation, and evolution of eukaryotic genes. We developed nucleosome occupancy and positioning data sets using leaf tissue of rice (Oryza sativa) and both leaf and flower tissues of Arabidopsis (Arabidopsis thaliana). We show that model plant and animal species share the fundamental characteristics associated with nucleosome dynamics. Only 12% and 16% of the Arabidopsis and rice genomes, respectively, were occupied by well-positioned nucleosomes. The cores of positioned nucleosomes were enriched with G/C dinucleotides and showed a lower C→T mutation rate than the linker sequences. We discovered that nucleosomes associated with heterochromatic regions were more spaced with longer linkers than those in euchromatic regions in both plant species. Surprisingly, different nucleosome densities were found to be associated with chromatin in leaf and flower tissues in Arabidopsis. We show that deep MNase-seq data sets can be used to map nucleosome occupancy of specific genomic loci and reveal gene expression patterns correlated with chromatin dynamics in plant genomes.
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 (T.Z., W.Z., J.J.); andNational Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (W.Z.).
authors.forename: Tao
authors.identifier: http://orcid.org/0000-0002-7897-0205
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 (T.Z., W.Z., J.J.); andNational Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (W.Z.).
authors.forename: Wenli
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 (T.Z., W.Z., J.J.); andNational Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (W.Z.) jjiang1@wisc.edu.
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D005075:Biological Evolution; D002843:Chromatin / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics*; D009928:Organ Specificity; D012275:Oryza / Q000235:genetics*
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes