title: Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning.
abstract: Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10- to 30-bp region from the dyad. S. pombe does not have a well-defined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the -1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.
authors.affiliation: Departments of Molecular Biosciences, Statistics, and Chemistry, Northwestern University, Evanston, IL 60208.
authors.forename: Georgette
authors.initials: G
authors.lastname: Moyle-Heyrman
authors.forename: Tetiana
authors.initials: T
authors.lastname: Zaichuk
authors.forename: Liqun
authors.initials: L
authors.lastname: Xi
authors.forename: Quanwei
authors.initials: Q
authors.lastname: Zhang
authors.forename: Olke C
authors.initials: OC
authors.lastname: Uhlenbeck
authors.forename: Robert
authors.initials: R
authors.lastname: Holmgren
authors.forename: Jonathan
authors.initials: J
authors.lastname: Widom
authors.forename: Ji-Ping
authors.initials: JP
authors.lastname: Wang
mesh_terms: D000225:Adenine / Q000378:metabolism; D001483:Base Sequence; D015825:Chromosomes, Fungal / Q000378:metabolism / Q000648:ultrastructure*; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000378:metabolism*; D009841:Oligonucleotides / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000378:metabolism; D012568:Schizosaccharomyces / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013941:Thymine / Q000378:metabolism
chemical_list: D009707:Nucleosomes; D009841:Oligonucleotides; D000225:Adenine; D013941:Thymine
keywords: chromatin structure; gene regulation; heterochromatin