title: The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere.
abstract: The centromeres of budding yeast are ~120 bp in size and contain three functional elements: an AT-rich region flanked by binding sites for Cbf1 and CBF3. A specialized nucleosome containing the H3 variant Cse4 (CenH3) is formed at the centromere. Our genome-wide paired-end sequencing of nucleosomal DNA reveals that the centromeric nucleosome contains a micrococcal nuclease-resistant kernel of 123-135 bp, depending on the centromere, and is therefore significantly shorter than the canonical nucleosome. Unlike canonical nucleosomes, the centromeric nucleosome is essentially perfectly positioned. The entire centromere is included, together with at least 1 bp of DNA upstream of the Cbf1 site and at least 4 bp downstream of the CBF3 site. The fact that the binding sites for Cbf1 and CBF3 are included within the centromeric nucleosome has important implications for models of the centromeric nucleosome and for kinetochore function.
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Hope A
authors.initials: HA
authors.lastname: Cole
authors.forename: Bruce H
authors.initials: BH
authors.lastname: Howard
authors.forename: David J
authors.initials: DJ
authors.lastname: Clark
mesh_terms: D001483:Base Sequence; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D002503:Centromere / Q000235:genetics* / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal / Q000235:genetics; D023281:Genomics / Q000379:methods; D006657:Histones / Q000235:genetics / Q000378:metabolism; D018386:Kinetochores / Q000378:metabolism; D008954:Models, Biological; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; C064042:CBF1 protein, S cerevisiae; C092348:CEP3 protein, S cerevisiae; C092746:CSE4 protein, S cerevisiae; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D006657:Histones; D009687:Nuclear Proteins; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins