title: High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.
abstract: We mapped nucleosome occupancy by paired-end Illumina sequencing in C. elegans embryonic cells, adult somatic cells, and a mix of adult somatic and germ cells. In all three samples, the nucleosome occupancy of gene promoters on the X chromosome differed from autosomal promoters. While both X and autosomal promoters exhibit a typical nucleosome-depleted region upstream of transcript start sites and a well-positioned +1 nucleosome, X-linked gene promoters on average exhibit higher nucleosome occupancy relative to autosomal promoters. We show that the difference between X and autosomes does not depend on the somatic dosage compensation machinery. Instead, the chromatin difference at promoters is partly encoded by DNA sequence, because a model trained on nucleosome sequence preferences from S. cerevisiae in vitro data recapitulate nearly completely the experimentally observed difference between X and autosomal promoters. The model predictions also correlate very well with experimentally determined occupancy values genome-wide. The nucleosome occupancy differences observed on X promoters may bear on mechanisms of X chromosome dosage compensation in the soma, and chromosome-wide repression of X in the germline.
authors.affiliation: Department of Biology, Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA. ercan@email.unc.edu
authors.forename: Sevinç
authors.initials: S
authors.lastname: Ercan
authors.forename: Yaniv
authors.initials: Y
authors.lastname: Lubling
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics*; D004303:Dosage Compensation, Genetic / Q000235:genetics; D050172:Genes, X-Linked; D008297:Male; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000378:metabolism*; D009876:Operon / Q000235:genetics; D011401:Promoter Regions, Genetic
chemical_list: D009707:Nucleosomes