title: Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast.
abstract: BACKGROUND
  The intrinsic DNA sequence is an important determinant of nucleosome positioning. Some DNA sequence patterns can facilitate nucleosome formation, while others can inhibit nucleosome formation. Nucleosome positioning influences the overall rate of sequence evolution. However, its impacts on specific patterns of sequence evolution are still poorly understood.
  
  
  RESULTS
  Here, we examined whether nucleosomal DNA and nucleosome-depleted DNA show distinct polymorphism patterns to maintain adequate nucleosome architecture on a genome scale in yeast. We found that sequence polymorphisms in nucleosomal DNA tend to facilitate nucleosome formation, whereas polymorphisms in nucleosome-depleted DNA tend to inhibit nucleosome formation, which is especially evident at nucleosome-disfavored sequences in nucleosome-free regions at both ends of genes. Sequence polymorphisms facilitating nucleosome positioning correspond to stable nucleosome positioning. These results reveal that sequence polymorphisms are under selective constraints to maintain nucleosome positioning.
  
  
  BACKGROUND
  zhimdai@gmail.com; issdxh@mail.sysu.edu.cn
authors.affiliation: Department of Electronic, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou 510006, China. zhimdai@gmail.com
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Dai
authors.forename: Xianhua
authors.initials: X
authors.lastname: Dai
authors.forename: Qian
authors.initials: Q
authors.lastname: Xiang
mesh_terms: D042002:Chromatin Assembly and Disassembly; D055106:Genome-Wide Association Study; D009707:Nucleosomes / Q000378:metabolism*; D011110:Polymorphism, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D009707:Nucleosomes