title: Transcriptional interaction-assisted identification of dynamic nucleosome positioning.
abstract: BACKGROUND
  Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucleosomes are dynamic in vivo.
  
  
  RESULTS
  Motivated by our observation that transcriptional interaction is discriminative information for nucleosome occupancy, we developed a novel computational approach to identify dynamic nucleosome positions at promoters by combining transcriptional interaction and genomic sequence information. Our approach successfully identified experimentally determined nucleosome positioning dynamics available in three cellular conditions, and significantly improved the prediction accuracy which is based on sequence information alone. We then applied our approach to various cellular conditions and established a comprehensive landscape of dynamic nucleosome positioning in yeast.
  
  
  CONCLUSIONS
  Analysis of this landscape revealed that the majority of nucleosome positions are maintained during most conditions. However, nucleosome occupancy at most promoters fluctuates with the corresponding gene expression level and is reduced specifically at the phase of peak expression. Further investigation into properties of nucleosome occupancy identified two gene groups associated with distinct modes of nucleosome modulation. Our results suggest that both the intrinsic sequence and regulatory proteins modulate nucleosomes in an altered manner.
authors.affiliation: Electronic Department, Sun Yat-Sen University, Guangzhou, 510275, PR 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
authors.forename: Jihua
authors.initials: J
authors.lastname: Feng
authors.forename: Yangyang
authors.initials: Y
authors.lastname: Deng
authors.forename: Jiang
authors.initials: J
authors.lastname: Wang
authors.forename: Caisheng
authors.initials: C
authors.lastname: He
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics; D023281:Genomics / Q000379:methods; D009707:Nucleosomes / Q000235:genetics*; D015203:Reproducibility of Results; D014158:Transcription, Genetic
chemical_list: D009707:Nucleosomes; D004247:DNA